add two molecular vis workflow cases from Helgi Ingolfsson

.gitignore

@@ -2,4 +2,5 @@
 .DS_Store
 upload_huggingface.py
 # only for github repo, not huggingface repo
-# sci_volume_data/**/*.raw
+# sci_volume_data/**/*.raw
+statistics/

eval_cases/molecular_vis/README.md

@@ -0,0 +1,29 @@
+# SciVisAgentBench: Molecular Visualization
+
+This benchmark is designed to evaluate agents on molecular visualization tasks, specifically focusing on tools like VMD (Visual Molecular Dynamics).
+
+## Overview
+
+The benchmark assesses agent capabilities across different levels of complexity:
+- **Basic Actions (Easy)**: Simple, atomic commands and operations (Currently implemented).
+- **Workflows (Medium)**: Sequences of actions forming a coherent pipeline (Planned).
+- **Scientific Tasks (Hard)**: Complex, goal-oriented scientific analysis and visualization (Planned).
+
+## Setup
+
+1. **Data Preparation**:
+   - Download the PDB file `1CRN` from the [RCSB PDB](https://www.rcsb.org/structure/1CRN).
+   - Place the downloaded file into the `data/` folder in this directory.
+
+## Usage
+
+You can run the evaluation cases defined in the YAML files (located in the `actions/` directory) using either:
+- **Promptfoo**
+- The **SciVisAgentBench Evaluation Framework**
+
+Refer to the [main repository](https://github.com/KuangshiAi/SciVisAgentBench/tree/main) for detailed instructions on running the evaluation harness.
+
+## Future Extensions
+
+### SciVisAgentBench: MD Simulations
+A placeholder for Molecular Dynamics (MD) simulation tasks is currently reserved. This will be expanded to include setting up, running, and analyzing simulations.

eval_cases/molecular_vis/actions/basic_actions.yaml

@@ -0,0 +1,633 @@
+# Basic Actions for Molecular Visualization Benchmark
+# These actions test core functionality of molecular visualization tools
+#https://www.rcsb.org/structure/1CRN
+
+# Loading a CIF file
+- vars:
+    question: |
+        Remove all molecules from and load the data "/Users/kuangshiai/Documents/ND-VIS/Code/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis/data/1CRN.cif".
+        Take a screenshot to confirm if the dataset has been loaded.
+        Respond with <1> if the cif file has been loaded and the molecule is visible in the viewport, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Basic visualization - Van der Waals representation
+- vars:
+    question: |
+        Change the visualization type to Van-der-Waals.
+        Take a screenshot to validate whether the representation has been changed.
+        Respond with <1> if the molecule in the viewport is in the Van-der-Waals representation, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Licorice representation
+- vars:
+    question: |
+        Change the visualization type to Licorice (stick representation).
+        Take a screenshot to validate whether the representation has been changed.
+        Respond with <1> if the molecule in the viewport is in the Licorice representation showing bonds as sticks, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Coloring by element
+- vars:
+    question: |
+        Color the molecule by element (atoms colored according to their chemical element).
+        Take a screenshot to validate whether the coloring has been applied.
+        Respond with <1> if the molecule is colored by element with different colors for different atom types, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Coloring by chain
+- vars:
+    question: |
+        Select chain A and color it red. Color all other chains blue.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if Chain A is colored red and other chains are colored blue, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Coloring by residue type
+- vars:
+    question: |
+        Color the molecule by residue type (amino acids colored according to their type).
+        Take a screenshot to validate whether the coloring has been applied.
+        Respond with <1> if the molecule is colored by residue type with different amino acids having distinct colors, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring specific residues
+- vars:
+    question: |
+        Select residues 1 to 10 and color them green. Keep the rest of the molecule in its current color.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if residues 1 to 10 are colored green while the rest of the molecule remains in a different color, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting specific atoms
+- vars:
+    question: |
+        Select all carbon atoms and color them cyan.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all carbon atoms are colored cyan while other atoms have different colors, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Multiple representations
+- vars:
+    question: |
+        Create two representations: show the backbone as Cartoon and all side chains as Licorice.
+        Take a screenshot to validate whether both representations are visible.
+        Respond with <1> if both representations are visible (Cartoon backbone + Licorice side chains), or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Material properties - Opaque
+- vars:
+    question: |
+        Change the material to Opaque (fully opaque, no transparency).
+        Take a screenshot to validate whether the material has been changed.
+        Respond with <1> if the molecule appears fully opaque with no transparency, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Changing representation radius
+- vars:
+    question: |
+        Change the representation to Licorice and set the radius to 0.3.
+        Take a screenshot to validate whether the radius has been changed.
+        Respond with <1> if the Licorice representation shows bonds with a radius of 0.3, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Coloring by B-factor (temperature factor)
+- vars:
+    question: |
+        Color the molecule by B-factor (temperature factor, showing flexibility/uncertainty).
+        Take a screenshot to validate whether the coloring has been applied.
+        Respond with <1> if the molecule is colored by B-factor showing a gradient of colors indicating different temperature factors, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting water molecules
+- vars:
+    question: |
+        Select all water molecules (residue name "HOH" or "WAT") and color them cyan.
+        Take a screenshot to validate whether the water molecules have been selected and colored.
+        Respond with <1> if all water molecules are colored cyan and visible in the viewport, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Coloring by charge
+- vars:
+    question: |
+        Color the molecule by charge (positive charges one color, negative charges another, neutral a third color).
+        Take a screenshot to validate whether the coloring has been applied.
+        Respond with <1> if the molecule is colored by charge with distinct colors for positive, negative, and neutral regions, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Coloring by hydrophobicity
+- vars:
+    question: |
+        Color the molecule by hydrophobicity (hydrophobic residues one color, hydrophilic another).
+        Take a screenshot to validate whether the coloring has been applied.
+        Respond with <1> if the molecule is colored by hydrophobicity with distinct colors for hydrophobic and hydrophilic regions, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and highlighting active site
+- vars:
+    question: |
+        Select residues within 5 Angstroms of residue 25 and color them yellow. Color the rest of the molecule gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if residues within 5 Angstroms of residue 25 are colored yellow and the rest of the molecule is colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting protein vs non-protein
+- vars:
+    question: |
+        Color all protein atoms green and all non-protein atoms (water, ions, ligands) red.
+        Take a screenshot to validate whether the coloring has been applied.
+        Respond with <1> if protein atoms are colored green and non-protein atoms (water, ions, ligands) are colored red, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Changing background color
+- vars:
+    question: |
+        Change the background color to white.
+        Take a screenshot to validate whether the background color has been changed.
+        Respond with <1> if the background of the viewport is white, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting specific atom types in a range
+- vars:
+    question: |
+        Select all oxygen atoms in residues 1 to 20 and color them red.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all oxygen atoms in residues 1 to 20 are colored red, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting atoms within distance
+- vars:
+    question: |
+        Select all atoms within 3 Angstroms of any atom in residue 15 and color them magenta.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all atoms within 3 Angstroms of residue 15 are colored magenta, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and hiding specific residues
+- vars:
+    question: |
+        Select residues 20 to 30 and hide them (make them invisible).
+        Take a screenshot to validate whether the residues have been hidden.
+        Respond with <1> if residues 20 to 30 are not visible in the viewport while the rest of the molecule remains visible, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and showing only specific atoms
+- vars:
+    question: |
+        Show only atoms with element type "N" (nitrogen) and hide all other atoms.
+        Take a screenshot to validate whether only nitrogen atoms are visible.
+        Respond with <1> if only nitrogen atoms are visible in the viewport and all other atoms are hidden, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and showing only backbone
+- vars:
+    question: |
+        Show only the backbone atoms (N, CA, C, O) as Licorice representation.
+        Take a screenshot to validate whether only backbone atoms are visible.
+        Respond with <1> if only backbone atoms (N, CA, C, O) are visible in Licorice representation and side chains are hidden, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and showing only side chains
+- vars:
+    question: |
+        Show only side chain atoms (excluding backbone atoms N, CA, C, O) as Van-der-Waals representation.
+        Take a screenshot to validate whether only side chain atoms are visible.
+        Respond with <1> if only side chain atoms are visible in Van-der-Waals representation and backbone atoms are hidden, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting aromatic residues
+- vars:
+    question: |
+        Select all aromatic residues (PHE, TYR, TRP) and color them purple.
+        Take a screenshot to validate whether the aromatic residues have been selected and colored.
+        Respond with <1> if all aromatic residues (PHE, TYR, TRP) are colored purple, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting charged residues
+- vars:
+    question: |
+        Select all charged residues (ARG, LYS, ASP, GLU) and color them red for positive charges and blue for negative charges.
+        Take a screenshot to validate whether the charged residues have been selected and colored correctly.
+        Respond with <1> if charged residues are colored correctly (ARG/LYS red, ASP/GLU blue), or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Multiple selections with different representations
+- vars:
+    question: |
+        Show the backbone as Cartoon colored by chain, and show all side chain atoms as Van-der-Waals colored by element.
+        Take a screenshot to validate whether both representations are visible with their respective colorings.
+        Respond with <1> if the backbone is shown as Cartoon colored by chain and side chain atoms are shown as Van-der-Waals colored by element, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom selection - backbone with sidechain by element
+- vars:
+    question: |
+        Show backbone atoms (N, CA, C, O) as Licorice colored blue, and show side chain atoms as Van-der-Waals colored by element.
+        Take a screenshot to validate whether both representations are visible with their respective colorings.
+        Respond with <1> if backbone atoms are shown as Licorice colored blue and side chain atoms are shown as Van-der-Waals colored by element, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by distance from specific atom
+- vars:
+    question: |
+        Select all atoms within 4 Angstroms of the CA atom of residue 10 and color them green. Color all other atoms gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all atoms within 4 Angstroms of the CA atom of residue 10 are colored green and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Coloring by atom selection with multiple criteria
+- vars:
+    question: |
+        Select all atoms that are either oxygen or nitrogen atoms in residues 1 to 20, and color them red. Color all other atoms gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all oxygen and nitrogen atoms in residues 1 to 20 are colored red and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom property
+- vars:
+    question: |
+        Select all atoms with element type "S" (sulfur) and color them yellow. Keep all other atoms in their default color.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all sulfur atoms are colored yellow while other atoms remain in their default color, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Coloring by residue number
+- vars:
+    question: |
+        Color the molecule by residue number (gradient from N-terminus to C-terminus).
+        Take a screenshot to validate whether the coloring has been applied.
+        Respond with <1> if the molecule is colored by residue number showing a gradient from the beginning to the end of the sequence, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom type in specific region
+- vars:
+    question: |
+        Select all nitrogen atoms in residues 5 to 15 and color them blue. Color all other atoms gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all nitrogen atoms in residues 5 to 15 are colored blue and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom selection - element and residue combination
+- vars:
+    question: |
+        Select all oxygen atoms in polar residues (SER, THR, ASN, GLN, TYR, CYS) and color them cyan. Color all other atoms gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all oxygen atoms in polar residues are colored cyan and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom selection - distance-based with element filter
+- vars:
+    question: |
+        Select all oxygen atoms within 5 Angstroms of residue 15 and color them red. Color all other atoms gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all oxygen atoms within 5 Angstroms of residue 15 are colored red and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom selection - backbone with sidechain by element
+- vars:
+    question: |
+        Show the backbone as NewCartoon colored by chain. Show all side chain carbon atoms as Licorice colored gray, all side chain nitrogen atoms as Licorice colored blue, and all side chain oxygen atoms as Licorice colored red.
+        Take a screenshot to validate whether the representations and colorings have been applied.
+        Respond with <1> if the backbone is shown as NewCartoon colored by chain, side chain carbon atoms are Licorice gray, side chain nitrogen atoms are Licorice blue, and side chain oxygen atoms are Licorice red, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom selection - complex distance and element
+- vars:
+    question: |
+        Select all carbon atoms within 4 Angstroms of any nitrogen atom in residues 1 to 15, and color them green. Color all other atoms gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all carbon atoms within 4 Angstroms of any nitrogen atom in residues 1 to 15 are colored green and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom selection - multiple criteria
+- vars:
+    question: |
+        Select all atoms that are either (carbon atoms in residues 1 to 10) or (nitrogen atoms in residues 11 to 20), and color them yellow. Color all other atoms gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all atoms matching the criteria are colored yellow and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom selection - complex multi-criteria
+- vars:
+    question: |
+        Select all atoms that are either (oxygen atoms in residues 1 to 10) or (nitrogen atoms within 3 Angstroms of residue 15), and color them magenta. Color all other atoms gray.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if all atoms matching the complex criteria are colored magenta and all other atoms are colored gray, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and showing only CA atoms
+- vars:
+    question: |
+        Show only CA (alpha carbon) atoms as Van-der-Waals spheres colored by chain.
+        Take a screenshot to validate whether only alpha carbons are visible.
+        Respond with <1> if only alpha carbon atoms are visible as spheres colored by chain, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and showing only heteroatoms
+- vars:
+    question: |
+        Show only heteroatoms (non-standard atoms like water, ions, ligands) as Van-der-Waals spheres colored by element.
+        Take a screenshot to validate whether only heteroatoms are visible.
+        Respond with <1> if only heteroatoms (non-standard atoms) are visible as spheres colored by element, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Selecting and coloring by atom selection - multiple element types
+- vars:
+    question: |
+        Select all carbon, nitrogen, and oxygen atoms and color them by element (carbon gray, nitrogen blue, oxygen red). Hide all other atoms.
+        Take a screenshot to validate whether the selection and coloring has been applied.
+        Respond with <1> if only carbon (gray), nitrogen (blue), and oxygen (red) atoms are visible and all other atoms are hidden, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true

eval_cases/molecular_vis/workflows/eval_analysis_workflows.yaml

@@ -0,0 +1,77 @@
+# Test Cases for SciVisAgentBench molecular visualization workflows
+# This test evaluates the ability to complete molecular visualization tasks
+# with detailed requirements and evaluation criteria
+
+# 1. Curved membrane simulation
+# As part of a protocol paper for building membrane using the coarse-grained Martini 3 force field, https://doi.org/10.1016/bs.mie.2024.03.010, a tutorial was developed: https://bbs.llnl.gov/data/building-membranes-data
+# Tutorial 4 is on curved membranes which is used here as an example of bilayer visualization. 
+- vars:
+    question: |
+        1. Please load the Martini coarse-grained simulation file from "curved-membrane/data/curved-membrane." into VMD.
+
+        2. Use VMD to show a zoomed in view of the membrane side coloring the water blue and the lipid phosphate (PO4 beads) red, and take a screenshot.
+
+        3. Analyze the visualization and answer the following questions:
+        Q1: Is there any water that penetrates into the membrane phase? (yes/no)
+        
+        4. Save your work:
+        Save the VMD state as "curved-membrane/results/{agent_mode}/curved-membrane.vmd".
+        Save the screenshot of the visualization as "curved-membrane/results/{agent_mode}/curved-membrane.png".
+        Save the answers to the analysis questions in plain text as "curved-membrane/results/{agent_mode}/answers.txt".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the visualization show a side view of a bilayer rather than a top-down or oblique view?
+          2. Is water present above and below the bilayer, with a mostly empty region in the middle corresponding to the bilayer core?
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+
+# Q1 reason: A few water molecules can be seen a little into the membrane.
+
+
+# 2. RAS-RAF on a plasma membrane
+# The RAS protein is lipid anchored and sits on the inner leaflet of the plasma membrane where it can bind RAF.
+# This is a snapshot of a RAS protein bound to the RBD and CRD domains of RAF on top of an eight-component plasma membrane setup with the coarse-grained Martini 2 force field.
+# This simulation frame is an example from the following study https://doi.org/10.1073/pnas.2113297119 and can be found online at: https://bbs.llnl.gov/data/ras-lipid-dependent-dynamics-data
+- vars:
+    question: |
+        1. Please load the Martini coarse-grained simulation file from "ras-raf-membrane/data/ras-raf-membrane.gro" into VMD. The simulations has a membrane and a RAS-RAF protein complex.
+        
+        2. Use VMD to show a zoomed in side view of the membrane and center on the protein with the protein below the membrane.
+        For the bilayer only show the PO4 lipids beads and ROH cholesterol bead and color them gray. 
+        Also show the protein back bone beads coloring RAS (resid 2 to 187) red and RAF (resid 188 to 329) blue.
+        Take a screenshot of the visualization.
+
+        3. Analyze the visualization and answer the following questions:
+        Q1: Are there any cholesterol head groups in the bilayer center? (yes/no)
+
+        Q2: How many lipids are there within 1.5 nm of the RAF protein?
+          A. 0
+          B. 0-3
+          C. 3-5
+          D. >5
+
+        4. Save your work:
+        Save the VMD state as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.vmd".
+        Save the screenshot of the visualization as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.png".
+        Save the answers to the analysis questions in plain text as "ras-raf-membrane/results/{agent_mode}/answers.txt".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Camera Position: Is the image centered on a protein complex composed of clearly distinguishable half red RAS and half blue RAF components?
+          2. Membrane Placement: Is a lipid bilayer clearly visible above the protein?
+          3. Correct Leaflet Ordering: Is the inner leaflet of the bilayer closer to the protein and the outer leaflet positioned farther away?
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: Yes
+          2. Q2 correct answer: C. 3-5
+
+# Q1 reason: quite some gray dots from cholesterol ROH headgroup bead can be seen in the center of the bilayer, so the answer is YES.
+# Q2 reason: if you run the flowing VMD selection command (name PO4 ROH) and within 15 of (index 3457 to 35009 and resid 188 to 329)
+# You will find 4 lipids head group beads, so the answer is C. 3-5 
+# Note here it’s important to only count each lipid once, e.g. either use a single reference bead per lipid or center of mass, also selecting the protein can be tricky as the lipids and water also if resid’s in the 188 to 329 range so either exclude other molecule or sub select only the protein residues

eval_cases/napari/0_actions/eval_basic_napari_functions.yaml

@@ -0,0 +1,486 @@
+# Basic Napari Function Tests - Action Level
+# These tests evaluate individual server functions with simple, single-function calls
+# Each test focuses on testing one specific function with appropriate parameters
+# We suggest using https://www.ebi.ac.uk/bioimage-archive/galleries/S-BIAD7.html IM1 as dataset_001
+# We suggest using https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/S-BIAD573.html IM1 as dataset_002
+
+# Test: open_file - Load a multi-dimensional image file (T, Z, Y, X, C)
+- vars:
+    question: |
+      Load the file "dataset_001/dataset_001.tiff" into the viewer.
+      Respond with <1> if the file was successfully loaded, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: delete layers - Delete all loaded layers from the viewer
+- vars:
+    question: |
+      Delete the all currently loaded layers.
+      Respond with <1> if all layers were successfully deleted, or <0> if the operation failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+    
+# Test: open_file - Load a single image file
+- vars:
+    question: |
+      Load the file "dataset_002/dataset_002.tif" into the viewer.
+      Respond with <1> if the file was successfully loaded, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: list_layers - Get information about loaded layers
+- vars:
+    question: |
+      Retrieve information about all currently loaded layers in the viewer.
+      Respond with <1> if you successfully retrieved layer information, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Z-stack Navigation - Scroll through different depths
+- vars:
+    question: |
+      Navigate through the z-stack of the loaded image. Use set_z_slice to jump to at least z-slice 0 to examine structures at different depths. 
+      Take a screenshot at each z-slice to verify navigation. 
+      Respond with <1> if you successfully navigated through different z-slices and could see structural changes, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+
+# Test: Time Series Navigation - Navigate through time points
+- vars:
+    question: |
+      If the data has time dimensions, use set_timestep to navigate through different time points.
+      Take screenshots at different time points to show temporal changes.
+      If no time dimension exists, simulate time navigation by adjusting the current view and taking multiple screenshots.
+      Respond with <1> if you successfully navigated through time points or simulated time navigation, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+    
+# Test: set_colormap - Change layer colormap
+- vars:
+    question: |
+      Change the colormap of the active image layer (dataset_002_ch1) to 'viridis'.
+      Respond with <1> if the colormap was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: set_opacity - Adjust layer transparency
+- vars:
+    question: |
+      Set the opacity of the active layer (dataset_002_ch1) to 0.5 (50% transparent).
+      Respond with <1> if the opacity was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: set_blending - Change layer blending mode
+- vars:
+    question: |
+      Change the blending mode of the active layer to 'additive'.
+      Respond with <1> if the blending mode was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: auto_contrast - Auto-adjust contrast
+- vars:
+    question: |
+      Automatically adjust the contrast of the active image layer.
+      Respond with <1> if the contrast was successfully auto-adjusted, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: set_contrast_limits - Set specific contrast limits
+- vars:
+    question: |
+      Set the contrast limits of the active layer to min=0.1 and max=0.9.
+      Respond with <1> if the contrast limits were successfully set, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: set_gamma - Adjust gamma correction
+- vars:
+    question: |
+      Set the gamma correction of the active layer to 1.5.
+      Respond with <1> if the gamma was successfully adjusted, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: set_interpolation - Change interpolation mode - doesn't work
+- vars:
+    question: |
+      Change the interpolation mode of the active layer to 'linear'.
+      Respond with <1> if the interpolation mode was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: toggle_view - Switch between 2D and 3D view
+- vars:
+    question: |
+      Switch the viewer to 3D mode.
+      Respond with <1> if the view was successfully switched to 3D, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: get_dims_info - Get dimension information
+- vars:
+    question: |
+      Get information about the viewer's current dimension settings.
+      Respond with <1> if you successfully retrieved dimension information, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: get_camera - Get current camera settings
+- vars:
+    question: |
+      Retrieve the current camera settings of the viewer.
+      Respond with <1> if you successfully retrieved camera settings, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: reset_camera - Reset camera to default view
+- vars:
+    question: |
+      Reset the camera to the default view.
+      Respond with <1> if the camera was successfully reset, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: set_camera - Adjust camera settings
+- vars:
+    question: |
+      Set the camera zoom to 2.0.
+      Respond with <1> if the camera zoom was successfully set, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: set_layer_visibility - Toggle layer visibility
+- vars:
+    question: |
+      Hide the active layer (set visible to false).
+      Respond with <1> if the layer visibility was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: set_layer_visibility - Show layer again
+- vars:
+    question: |
+      Show the active layer again (set visible to true).
+      Respond with <1> if the layer visibility was successfully changed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: screenshot - Take a screenshot
+- vars:
+    question: |
+      Take a screenshot of the current view.
+      Respond with <1> if the screenshot was successfully taken, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# # Test: get_layer_statistics - Get layer statistics
+# - vars:
+#     question: |
+#       Retrieve basic statistics (min, max, mean, std) for the active layer.
+#       Respond with <1> if you successfully retrieved layer statistics, or <0> if it failed. Only respond with <1> or <0>.
+#   assert:
+#     - type: contains-all
+#       value: "<1>"
+#     - type: not-contains
+#       value: "<0>"
+#   options:
+#     cache: false
+#     runSerially: true
+
+# # Test: add_points - Add point annotations - doesn't work
+# - vars:
+#     question: |
+#       Add two point markers at coordinates [[100, 100], [200, 200]] with the name "test_points".
+#       Respond with <1> if the points were successfully added, or <0> if it failed. Only respond with <1> or <0>.
+#   assert:
+#     - type: contains-all
+#       value: "<1>"
+#     - type: not-contains
+#       value: "<0>"
+#   options:
+#     cache: false
+#     runSerially: true
+
+# Test: add_shapes - Add shape annotations
+- vars:
+    question: |
+      Add a rectangle shape with coordinates [[[50, 50], [150, 50], [150, 150], [50, 150]]] and name "test_rectangle".
+      Respond with <1> if the shape was successfully added, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# # Test: measure_distance - Measure distance between points - doesn't work 
+# - vars:
+#     question: |
+#       Measure the distance between point [100, 100] and point [200, 200].
+#       Respond with <1> if the distance was successfully measured, or <0> if it failed. Only respond with <1> or <0>.
+#   assert:
+#     - type: contains-all
+#       value: "<1>"
+#     - type: not-contains
+#       value: "<0>"
+#   options:
+#     cache: false
+#    runSerially: true
+
+# Test: set_scale_bar - Show scale bar
+- vars:
+    question: |
+      Show the scale bar with unit 'um'.
+      Respond with <1> if the scale bar was successfully shown, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# # Test: set_axis_labels - Set axis labels - doesn't work
+# - vars:
+#     question: |
+#       Set axis labels to ['y', 'x'] for the 2D data.
+#       Respond with <1> if the axis labels were successfully set, or <0> if it failed. Only respond with <1> or <0>.
+#   assert:
+#     - type: contains-all
+#       value: "<1>"
+#     - type: not-contains
+#       value: "<0>"
+#   options:
+#     cache: false
+#     runSerially: true
+
+# Test: screenshot - Save screenshot to file
+- vars:
+    question: |
+      Save a screenshot.
+      Respond with <1> if the screenshot was successfully exported, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: save_layers - Save layer to file
+- vars:
+    question: |
+      Save the active layer to the file "test_layer.tif".
+      Respond with <1> if the layer was successfully saved, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: remove_layer - Remove a layer
+- vars:
+    question: |
+      Remove the layer named "test_rectangle".
+      Respond with <1> if the layer was successfully removed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Error handling - Try to load non-existent file
+- vars:
+    question: |
+      Try to load the non-existent file "nonexistent.tif" and handle the error gracefully.
+      Respond with <1> if the error was handled gracefully (no crash), or <0> if it crashed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Error handling - Try to remove non-existent layer
+- vars:
+    question: |
+      Try to remove a layer that doesn't exist named "nonexistent_layer" and handle the error gracefully.
+      Respond with <1> if the error was handled gracefully (no crash), or <0> if it crashed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: 3D View and Iso-surface Rendering
+- vars:
+    question: |
+      Enable iso-surface rendering for the loaded layer.
+      Take a screenshot to verify the 3D iso-surface rendering.
+      Respond with <1> if the 3D iso-surface rendering was successfully set up, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Cleanup - Remove remaining test layers
+- vars:
+    question: |
+      Remove the layer named "test_rectangle" to clean up test annotations.
+      Respond with <1> if the layer was successfully removed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true

eval_cases/napari/1_workflows/eval_analysis_workflows.yaml

@@ -0,0 +1,101 @@
+# Analysis Workflow Tests for napari-mcp
+# These tests evaluate complex analysis workflows that combine multiple napari functions
+# Each test focuses on performing specific analysis tasks
+
+# Test: Cell Counting and Measurement Analysis
+- vars:
+    question: |
+      Load the image "dataset_001/dataset_001.tiff" and set it to magenta colormap.
+      Take a screenshot and analyze it to count how many complete cells are visible (not cut off by edges).
+      Add point annotations to mark the center of each counted cell.
+      Measure the distance between the two most distant cells.
+      Respond with the number of complete cells you counted, for example "5" if you see 5 complete cells.
+  assert:
+    - type: llm-rubric
+      value: 
+        - It counted 2 complete cells
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Statistical Analysis and Data Export
+- vars:
+    question: |
+      Get basic statistics (min, max, mean, std) for the loaded layer.
+      Extract the raw layer data and examine its properties.
+      Save the current layer to a file for further analysis.
+      Export a screenshot of the current view for documentation.
+      Respond with <1> if the statistical analysis and data export were successful, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Annotation and Measurement Workflow
+- vars:
+    question: |
+      Add point annotations to mark specific features of interest in the image.
+      Add shape annotations (rectangles or circles) to highlight regions of interest.
+      Measure distances between multiple pairs of points.
+      Take a screenshot showing all annotations and measurements.
+      Respond with <1> if the annotation and measurement workflow was successful, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Time Series Analysis (if applicable)
+- vars:
+    question: |
+      If the data has time dimensions, navigate through different time points.
+      Compare cellular structures between different time points.
+      Take screenshots at different time points to show temporal changes.
+      If no time dimension exists, simulate time series analysis by adjusting the current view and taking multiple screenshots.
+      Respond with <1> if the time series analysis was successful, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Data Cropping and Region of Interest Analysis
+- vars:
+    question: |
+      Define a region of interest by cropping the layer to a specific area.
+      Analyze the cropped region separately from the full dataset.
+      Compare statistics between the full dataset and the cropped region.
+      Take screenshots of both the full view and the cropped region.
+      Respond with <1> if the cropping and region analysis was successful, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Cleanup - Reset for next test run
+- vars:
+    question: |
+      Delete all loaded layers and remove any annotations to prepare for the next test run.
+      Respond with <1> if all layers and annotations were successfully removed, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true

eval_cases/napari/1_workflows/eval_figure_recreation.yaml

@@ -0,0 +1,24 @@
+# Figure Recreation Tests for napari-mcp
+# These tests evaluate the agent's ability to recreate scientific figures from papers
+# Focus: Loading data, applying appropriate visualization settings, and matching target figures
+
+#Test: Recreate a figure from a dataset. 
+- vars:
+    question: |
+      Load the dataset into napari: dataset_001/dataset_001.tiff
+      Read the target figure: dataset_001/dataset_001.png but don't load it into napari.
+      Read the dataset description: dataset_001/dataset_001.yaml. 
+      Set the same colormaps and blending modes as the target figure.
+      Adjust contrast and gamma as needed to match the target figure.
+      Take a screenshot of your recreation.
+      If the recreation does not match the target figure, adjust the visualization settings and take a screenshot again.
+      Stop when the recreation matches the target figure or you have tried five different visualization settings.
+      Respond with <1> if you successfully recreated the figure and it closely matches the target, or <0> if it failed or doesn't match well. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true

eval_cases/napari/1_workflows/eval_iso_surface_determination.yaml

@@ -0,0 +1,22 @@
+# finding iso surface value for a dataset
+# These tests evaluate the agent's ability to recreate scientific figures from papers
+
+# Test: Iso surface determination for a target
+- vars:
+    question: |
+      Read the file "dataset_003/eval_iso_surface_determination_target_1.txt" to get the target iso-surface values for different tooth structures.
+      Load dataset_003/dataset_003.tif into napari. 
+      Switch to 3D view mode and set the rendering to iso. 
+      Find the iso surface value that shows the target clearly.
+      Rotate the camera to several angles and take a screenshot of the result each time to check if the target structure is clearly visible from different angles.
+      If the target structure is not clearly visible, adjust the iso surface value and take a screenshot again.
+      Stop when the target structure is clearly visible or you have tried five different iso surface values.
+      Respond with <1> if you clearly see the target structure, or <0> if you cannot see the target structure. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true

eval_cases/napari/1_workflows/eval_visualization_workflows.yaml

@@ -0,0 +1,103 @@
+# Basic Visualization Workflow Tests
+# Use https://www.ebi.ac.uk/bioimage-archive/galleries/S-BIAD7.html IM1 to test the workflows.
+
+# Test: Multi-channel Overlay with Colormaps with channels
+- vars:
+    question: |
+      Load the "dataset_001/dataset_001.tiff" dataset into napari. 
+      Depending on the number of channels, set the colormap for each channel to the corresponding color.
+      Use additive blending for all channels to create an overlay visualization.
+      Take a screenshot of the result.
+      Respond with <1> if all channels are visible with their respective colors in the overlay, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Hide All Channels Except for the Channel with the Cells
+- vars:
+    question: |
+      Set all layers invisible except for the layer that contains the individual cells. 
+      Take a screenshots to check if only individual cell bodies are shown.
+      Respond with <1> if only individual cell bodies are shown, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Contrast and Gamma Adjustment to Display Nucleus
+- vars:
+    question: |
+      Adjust the gamma value in channel 0 so that the bright cell organelles are only visible but the cell membrane is suppressed.  
+      Take screenshots to check if the contrast and gamma adjustments were successful.
+      Respond with <1> if the contrast and gamma adjustments were successful, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+
+# Test: Advanced 3D Camera Control and Navigation
+- vars:
+    question: |
+      Start with the default 3D view and take an initial screenshot.
+      Rotate the camera to show the 3D data from a different perspective (side view).
+      Take a screenshot to verify the 3D camera rotation.
+      Zoom in on the 3D structures so they appear larger in the viewport.
+      Take a screenshot to verify the 3D zoom.
+      Pan the camera to move the 3D view to show a different region.
+      Take a screenshot to verify the 3D pan.
+      Reset the camera to the default 3D view.
+      Take a final screenshot to verify the 3D reset.
+      Respond with <1> if all 3D camera operations were successful, or <0> if any failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Iso-surface Threshold Adjustment
+- vars:
+    question: |
+      Adjust the iso-surface threshold to different values to explore different surface levels.
+      Start with a low threshold (e.g., 0.1) and take a screenshot.
+      Increase the threshold to a medium value (e.g., 0.5) and take a screenshot.
+      Increase the threshold to a high value (e.g., 0.9) and take a screenshot.
+      Respond with <1> if you successfully adjusted iso-surface thresholds and could see different surface levels, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true
+
+# Test: Cleanup - Reset for next test run
+- vars:
+    question: |
+      Delete all loaded layers and reset the view to 2D mode to prepare for the next test run.
+      Respond with <1> if all layers were successfully deleted and the view was reset, or <0> if it failed. Only respond with <1> or <0>.
+  assert:
+    - type: contains-all
+      value: "<1>"
+    - type: not-contains
+      value: "<0>"
+  options:
+    cache: false
+    runSerially: true

eval_cases/paraview/category_specific_cases.yaml

@@ -0,0 +1,218 @@
+# Medical/Anatomical Data Visualization Test Cases for SciVisAgentBench
+# Tests scalar volume visualization capabilities for medical imaging data
+
+# Test 1: Basic Volume Rendering and Tissue Identification
+- vars:
+    question: |
+      Clear the ParaView pipeline and load the data file "foot/data/foot_256x256x256_uint8.raw".
+      1. Enable volume rendering to visualize the internal structures
+      2. Adjust the opacity transfer function to reveal both bone and soft tissue (bone should be more opaque, soft tissue semi-transparent)
+      3. Set an appropriate color map to differentiate tissue types (e.g., white/beige for bone, reddish for soft tissue)
+      Finally, save the paraview state as "foot/results/{agent_mode}/foot.pvsm"
+  assert:
+    - type: llm-rubric
+      value: |
+        - Successfully load the foot dataset
+        - Enable volume rendering
+        - Adjust opacity to show both bone and soft tissue structures
+        - Apply appropriate color mapping for tissue differentiation
+        - Use screenshot to verify foot bones (metatarsals, phalanges) and soft tissue are visible
+        - Verify the colors match the instruction (white/beige for bone, reddish for soft tissue)
+
+# # Test 2: Multi-Isosurface Segmentation
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "mri_ventricles/data/mri_ventricles_256x256x124_uint8.raw".
+#       1. Create at least 3 different isosurfaces at different threshold values to segment different tissue types
+#       2. Color each isosurface differently to distinguish structures
+#       3. Make appropriate surfaces semi-transparent if needed to show internal structures
+#       Finally, save the paraview state as "mri_ventricles/results/{agent_mode}/mri_ventricles.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+#         - Create multiple isosurfaces (at least 3) at different threshold values
+#         - Apply different colors to each isosurface for clear distinction
+#         - Use screenshot to verify brain ventricles are successfully segmented and visible
+#         - Verify transparency is applied where needed to show nested structures
+#         - Report identification of brain structures (ventricles, grey/white matter boundaries)
+
+# # Test 3: Cross-Sectional Analysis
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "skull/data/skull_256x256x256_uint8.raw".
+#       1. Create three orthogonal slices (axial, sagittal, and coronal planes)
+#       2. Position the slices to show key anatomical features of the skull
+#       3. Apply an appropriate color map to the slices
+#       Finally, save the paraview state as "skull/results/{agent_mode}/skull.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - Create exactly three orthogonal slices (axial, sagittal, coronal)
+#         - Use screenshot to verify all three slice planes are visible simultaneously
+#         - Verify slices show key features: cranial cavity, eye sockets, nasal cavity
+#         - Report which anatomical features are visible in each specific plane
+
+# # Test 4: Vascular Structure Visualization
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "aneurism/data/aneurism_256x256x256_uint8.raw".
+#       1. Use appropriate visualization technique to isolate and display the vascular structure
+#       2. Create an isosurface that clearly shows the aneurysm and blood vessels
+#       3. Apply a red or red-gradient color map appropriate for vascular visualization
+#       4. Compute and report the surface area of the vascular structure
+#       Finally, save the paraview state as "aneurism/results/{agent_mode}/aneurism.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - Successfully isolate vascular structure using isosurface
+#         - Use screenshot to verify aneurysm bulge is clearly visible
+#         - Verify red/red-gradient coloring is applied to vessels
+#         - Successfully compute and report numerical surface area value
+
+# # Test 5: Histogram Analysis and Tissue Classification
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "pancreas/data/pancreas_240x512x512_int16.raw".
+#       1. Generate a histogram of the intensity values with 256 bins
+#       2. Based on the histogram, identify distinct peaks corresponding to different tissue types
+#       3. Create threshold filters to isolate pancreatic tissue based on the histogram analysis
+#       4. Apply volume rendering with opacity settings based on your histogram findings
+#       Finally, save the paraview state as "pancreas/results/{agent_mode}/pancreas.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - Successfully generate histogram with 256 bins
+#         - Report specific intensity values for identified peaks
+#         - Create threshold filters using values derived from histogram peaks
+#         - Apply volume rendering with opacity based on histogram analysis
+#         - Use screenshot to verify pancreatic tissue is properly isolated
+
+# # Test 6: Complex Organ System Visualization
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "mri_woman/data/mri_woman_256x256x109_uint16.raw".
+#       1. Enable volume rendering to show internal anatomy
+#       2. Adjust the transfer functions to visualize multiple organ systems simultaneously
+#       3. Create a clip plane to show a sagittal cross-section while maintaining volume rendering
+#       4. Use appropriate color and opacity settings to distinguish between organs
+#       Finally, save the paraview state as "mri_woman/results/{agent_mode}/mri_woman.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - Enable volume rendering successfully
+#         - Adjust transfer functions to reveal multiple organ systems
+#         - Create clip plane in sagittal orientation
+#         - Use screenshots from anterior and lateral views to verify organ visibility
+#         - List identified organs (e.g., heart, lungs, liver, spine)
+#         - Verify clip plane and volume rendering work together
+
+# # Test 7: Small Animal Specimen Analysis
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "frog/data/frog_256x256x44_uint8.raw".
+#       1. Create visualization showing both skeletal and soft tissue structures
+#       2. Use either multiple isosurfaces or volume rendering with careful transfer functions
+#       3. Generate a plot-over-line measurement through the specimen (dorsal to ventral)
+#       Finally, save the paraview state as "frog/results/{agent_mode}/frog.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - Choose appropriate technique (isosurfaces or volume rendering)
+#         - Use screenshot to verify both skeleton and soft tissue are visible
+#         - Successfully create plot-over-line from dorsal to ventral
+#         - Report numerical values from plot-over-line measurement
+#         - Verify measurement traverses through the specimen correctly
+
+# # Test 8: Dental Structure Analysis
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "tooth/data/tooth_103x94x161_uint8.raw".
+#       1. Create isosurface to show the tooth enamel (outer layer)
+#       2. Use volume rendering or additional isosurface to show internal structures (dentin, pulp cavity)
+#       3. Apply appropriate colors (white for enamel, yellow for dentin)
+#       Finally, save the paraview state as "tooth/results/{agent_mode}/tooth.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - Create isosurface at appropriate threshold for enamel
+#         - Use screenshot to verify white color on enamel and yellow/amber color on dentin
+#         - Identify enamel, dentin, and pulp cavity structures
+
+# # Test 9: Abdominal CT with Vascular Stent Visualization
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "stent/data/stent_512x512x174_uint16.raw".
+#       This is an abdominal/pelvic CT scan containing a stent in the abdominal aorta (no contrast agent used).
+#       1. Create a volume rendering to show the overall abdominal anatomy
+#       2. Adjust the opacity transfer function to visualize bones (spine, pelvis) and soft tissue
+#       3. Create an isosurface at a high threshold value to isolate and highlight the metallic stent
+#       4. Apply appropriate colors - bone white/beige, soft tissue reddish, metallic grey for the stent
+#       Finally, save the paraview state as "stent/results/{agent_mode}/stent.pvsm"
+
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - Create volume rendering of full abdomen/pelvis
+#         - Use screenshot to verify spine and pelvis are visible
+#         - Create high-threshold isosurface to isolate metallic stent
+#         - Verify stent appears with metallic/grey coloring
+        
+# # # Test 10: Comparative Analysis with State Saving
+# # - vars:
+# #     question: |
+# #       Clear the ParaView pipeline and load the data file "vis_male/data/vis_male_128x256x256_uint8.raw".
+# #       1. Create two different visualization approaches:
+# #          a) Volume rendering optimized for soft tissue
+# #          b) Isosurface extraction for skeletal system
+# #       2. Save the ParaView state file to preserve your visualization setup
+# #       3. Create a text report comparing the effectiveness of both techniques
+# #   assert:
+# #     - type: llm-rubric
+# #       value: |
+# # 
+# #         - Create volume rendering with soft tissue emphasis
+# #         - Create separate isosurface for skeletal system
+# #         - Use screenshots to document both approaches
+# #         - Successfully save .pvsm state file
+# #         - Write and save comparative analysis as text file
+# #         - Report specific advantages/disadvantages of each technique
+# #         - Verify both visualizations show distinct anatomical features
+
+# # Test 11: Marine Biology Specimen
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "lobster/data/lobster_301x324x56_uint8.raw".
+#       1. Create visualization showing the exoskeleton and internal anatomy
+#       2. Adjust the visualization to show the prominent structure
+#       Finally, save the paraview state as "lobster/results/{agent_mode}/lobster.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - Choose appropriate visualization for exoskeleton (isosurface or volume)
+#         - Use screenshot to verify whether specific features can be identified: claws, abdomen, tail fan
+
+# # Test 12: Fish Anatomy Visualization  
+# - vars:
+#     question: |
+#       Clear the ParaView pipeline and load the data file "carp/data/carp_256x256x512_uint16.raw".
+#       1. Enable volume rendering to show internal fish anatomy
+#       2. Adjust transfer functions to reveal skeletal structure and organs
+#       3. Create a sagittal slice through the fish body
+#       4. Use color mapping that differentiates tissue types
+#       5. Reset camera with appropriate padding to frame the entire fish
+#       Finally, save the paraview state as "carp/results/{agent_mode}/carp.pvsm"
+#   assert:
+#     - type: llm-rubric
+#       value: |
+
+#         - The volume rendering show both skeleton and organs
+#         - Create sagittal slice along fish body length
+#         - Verify sagittal slice shows internal structure along body axis

eval_cases/paraview/chatvis_bench_cases.yaml

@@ -0,0 +1,430 @@
+# 1. line-plot
+- vars:
+    question: |
+          Read the dataset in the file "line-plot/data/line-plot.ex2", and print the number of components and the range of all the variables.
+          Show a default view of the dataset, colored by the variable Pres.
+          Create a line plot over all the variables in the dataset, from (0,0,0) to (0,0,10).
+          Write the values of the line plot in the file "line-plot/results/{agent_mode}/line-plot.csv", and save a screenshot of the line plot in "line-plot/results/{agent_mode}/line-plot.png".
+          Finally, save the ParaView state as "line-plot/results/{agent_mode}/line-plot.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Line Visualization Quality: Are multiple distinct lines clearly visible and properly rendered showing the evolution of different variables along the specified path?
+
+          2. Variable Differentiation: Are all dataset variables visually distinguishable through distinct colors or line styles with clear separation between curves?
+
+          3. Axis and Scale Appropriateness: Do the plot axes display appropriate ranges and scaling that effectively show the data trends and variations?
+
+          4. Legend and Readability: Is there a clear legend identifying each variable line with readable labels and proper visual organization?
+
+# 2. ml-dvr
+- vars:
+    question: |
+          Read in the file named "ml-dvr/data/ml-dvr.vtk", and generate a volume rendering using the default transfer function.
+          Save a screenshot, size 1920 x 1080 pixels, of an isometric view of the visualization in "ml-dvr/results/{agent_mode}/ml-dvr.png".
+          Finally, save the ParaView state as "ml-dvr/results/{agent_mode}/ml-dvr.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Volume Rendering Quality: Is the volume rendering properly generated with appropriate opacity and color mapping that reveals internal structures?
+
+          2. Transfer Function Application: Does the default transfer function effectively highlight meaningful data features and provide good visual contrast?
+
+          3. Isometric View Setup: Is the visualization displayed from an isometric viewpoint that provides a clear three-dimensional perspective of the volume?
+
+          4. Visual Clarity and Detail: Are the volume details clearly visible with proper lighting and shading that enhances depth perception?
+
+# 3. ml-iso
+- vars:
+    question: |
+          Read in the file named "ml-iso/data/ml-iso.vtk", and generate an isosurface of the variable var0 at value 0.5.
+          Save a screenshot of the result, size 1920 x 1080 pixels, in "ml-iso/results/{agent_mode}/ml-iso.png".
+          Finally, save the ParaView state as "ml-iso/results/{agent_mode}/ml-iso.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Isosurface Generation: Is the isosurface properly generated at the specified value (0.5) with correct topology and continuity?
+
+          2. Surface Rendering Quality: Does the isosurface display smooth surfaces with appropriate shading and lighting that reveals the 3D structure?
+
+          3. Geometric Accuracy: Are the surface features geometrically correct and free from artifacts or discontinuities?
+
+          4. Visual Presentation: Is the isosurface clearly visible with good contrast and coloring that enhances the understanding of the data structure?
+
+# 4. ml-slice-iso
+- vars:
+    question: |
+          Read in the file named "ml-slice-iso/data/ml-slice-iso.vtk", slice the volume with a y-z plane at x=0, and take a contour, colored red, through the slice at the value 0.5.
+          Save a screenshot of a +x direction view, size 1920 x 1080 pixels, of the result in "ml-slice-iso/results/{agent_mode}/ml-slice-iso.png".
+          Finally, save the ParaView state as "ml-slice-iso/results/{agent_mode}/ml-slice-iso.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Slice Generation: Is the y-z plane slice properly generated at x=0 position showing the correct cross-section of the volume?
+
+          2. Contour on Slice: Are the contour lines at value 0.5 correctly extracted from the slice and properly displayed?
+
+          3. Red Color Application: Is the contour visualization properly colored red as specified in the requirements?
+
+          4. View Direction: Is the visualization displayed from the correct +x direction view that provides clear visibility of the slice and contours?
+
+# 5. points-surf-clip
+- vars:
+    question: |
+          Read in the file named "points-surf-clip/data/points-surf-clip.ex2", generate a 3D Delaunay triangulation of the dataset, and clip with a y-z plane at x=0, keeping the -x half of the data.
+          Save a screenshot of the result as a wireframe, image size 1920 x 1080 pixels, in "points-surf-clip/results/{agent_mode}/points-surf-clip.png".
+          Finally, save the ParaView state as "points-surf-clip/results/{agent_mode}/points-surf-clip.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Delaunay Triangulation Quality: Is the 3D Delaunay triangulation properly generated creating a valid mesh structure from the point data?
+
+          2. Clipping Accuracy: Is the mesh correctly clipped by the y-z plane at x=0, with only the -x half of the data remaining visible?
+
+          3. Wireframe Representation: Is the result displayed as a clear wireframe showing the triangulated mesh structure with visible edges?
+
+          4. Geometric Integrity: Does the clipped wireframe maintain proper connectivity and show the expected geometric features without artifacts?
+
+# 6. shrink-sphere
+- vars:
+    question: |
+          Create a default sphere, hide it, and create a shrink filter from the sphere.
+          Double the sphere's theta resolution while halving the shrink filter's shrink factor.
+          Group the shrink filter and a wireframe of the sphere together, and save a screenshot of the result in "shrink-sphere/results/{agent_mode}/shrink-sphere.png", size 1920 x 1080 pixels with a white background.
+          Finally, save the ParaView state as "shrink-sphere/results/{agent_mode}/shrink-sphere.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Sphere Creation and Resolution: Is the sphere created with doubled theta resolution providing higher geometric detail and smoother curvature?
+
+          2. Shrink Filter Application: Is the shrink filter properly applied with halved shrink factor creating visible separation between mesh elements?
+
+          3. Dual Representation: Are both the wireframe sphere and shrink filter results simultaneously visible and properly grouped together?
+
+          4. Visual Quality: Does the visualization clearly show the contrast between the wireframe structure and the shrunken elements with appropriate white background?
+
+# 7. stream-glyph
+- vars:
+    question: |
+          Read in the file named "stream-glyph/data/stream-glyph.ex2", and trace streamlines of the V variable seeded from a default point cloud.
+          Render the streamlines with tubes, adding cone glyphs to the streamlines, and coloring the streamlines and glyphs by the Temp variable.
+          Save a screenshot of a +x view of the result, size 1920 x 1080 pixels, in "stream-glyph/results/{agent_mode}/stream-glyph.png".
+          Finally, save the ParaView state as "stream-glyph/results/{agent_mode}/stream-glyph.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Streamline Generation: Are streamlines properly traced following the V variable flow field with appropriate seeding from the point cloud?
+
+          2. Tube and Glyph Rendering: Are streamlines rendered as tubes with cone glyphs properly attached showing flow direction and magnitude?
+
+          3. Temperature Color Mapping: Are both streamlines and glyphs correctly colored by the Temp variable with appropriate color scaling?
+
+          4. View Configuration: Is the visualization displayed from the correct +x view direction providing clear visibility of the flow patterns and structures?
+
+# 8. time-varying
+- vars:
+    question: |
+          Read the dataset in the file "time-varying/data/time-varying.ex2", and color the data by the EQPS variable.
+          Viewing in the +y direction, play an animation through the time steps, with visible color bar legend.
+          Rescale the data range to last time step, and play the animation again.
+          Create a second linked render view to the right of the first, applying a temporal interpolator to the second view.
+          Play the animation simultaneously in both views, and save the animation of both views in "time-varying/results/{agent_mode}/time-varying.avi".
+          Print the following statistics: average value of EQPS over all locations and all time steps, average value of EQPS over all locations in the first half of the time steps, average value of EQPS over all locations in the even numbered time steps, and variance of EQPS over all locations and all the time steps.
+          Finally, save the ParaView state as "time-varying/results/{agent_mode}/time-varying.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Temporal Animation Quality: Does the animation smoothly progress through all time steps showing the evolution of the EQPS variable over time?
+
+          2. Dual View Configuration: Are both render views properly configured with the second view showing temporal interpolation effects compared to the first?
+
+          3. Color Mapping and Legend: Is the EQPS variable properly color-mapped with an appropriate color bar legend visible throughout the animation?
+
+          4. View Direction and Layout: Is the +y direction view properly set and are both views arranged side-by-side in the correct layout configuration?
+
+# 9. chart-opacity
+- vars:
+    question: |
+          Create a wavelet object.
+          Create a plot over line chart from the wavelet with three paths: arc_length, Points_Z, and RTData variables with opacity for arc_length 1 and opacity for Points_Z and RTData 0.3.
+          Save a screenshot in "chart-opacity/results/{agent_mode}/chart-opacity.png".
+          Finally, save the ParaView state as "chart-opacity/results/{agent_mode}/chart-opacity.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Chart Generation: Is the plot over line chart properly created from the wavelet data showing all three specified variables?
+
+          2. Variable Display: Are arc_length, Points_Z, and RTData variables all correctly plotted and distinguishable in the chart?
+
+          3. Opacity Settings: Is the arc_length variable displayed with full opacity (1.0) while Points_Z and RTData show reduced opacity (0.3)?
+
+          4. Chart Clarity: Does the chart provide clear visualization of the data trends with appropriate axis scaling and readable formatting?
+
+# 10. color-blocks
+- vars:
+    question: |
+          Read the file "color-blocks/data/color-blocks.ex2".
+          Color the dataset by the vtkBlockColors field.
+          Retrieve the color map, opacity transfer function, and 2D transfer function for vtkBlockColors.
+          Set block coloring for the block at /IOSS/element_blocks/block_2 using the x component of the ACCL variable.
+          Rescale the block's color and opacity maps to match the current data range of block_2.
+          For the ACCL variable of block_2, retrieve the color transfer function, enable the color bar, and apply cool to warm coloring.
+          View the entire dataset in the -y direction, and save a screenshot with blue-gray background in "color-blocks/results/{agent_mode}/color-blocks.png".
+          Finally, save the ParaView state as "color-blocks/results/{agent_mode}/color-blocks.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Block Color Mapping: Is the dataset properly colored by vtkBlockColors field with distinct block visualization?
+
+          2. Individual Block Coloring: Is block_2 correctly colored using the x component of the ACCL variable with appropriate scaling?
+
+          3. Color Transfer Functions: Are the color transfer functions properly applied with cool to warm coloring for the ACCL variable?
+
+          4. View Configuration: Is the dataset displayed from the -y direction with blue-gray background and visible color bar legend?
+
+# 11. color-data
+- vars:
+    question: |
+          Create a wavelet object.
+          Create a new calculator with the function 'RTData*iHat + ln(RTData)*jHat + coordsZ*kHat'.
+          Get a color transfer function/color map and opacity transfer function/opacity map for the result of the calculation, scaling the color and/or opacity maps to the data range.
+          For a surface representation, color by the x coordinate of the result using a cool to warm color map, show the color bar/color legend, and save a screenshot of size 1158 x 833 pixels in "color-data/results/{agent_mode}/color-data.png".
+          Finally, save the ParaView state as "color-data/results/{agent_mode}/color-data.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Calculator Function: Is the calculator properly implemented with the specified vector function combining RTData and coordinate components?
+
+          2. Color Transfer Function: Is the color transfer function correctly applied with cool to warm color mapping scaled to the data range?
+
+          3. Surface Coloring: Is the surface representation properly colored by the x coordinate of the calculated result?
+
+          4. Color Bar Display: Is the color bar/legend visible and properly displaying the color mapping scale and values?
+
+# 12. export-gltf
+- vars:
+    question: |
+          Create a wavelet object.
+          Create a surface rendering of the wavelet object and color by RTData.
+          Scale the color map to the data, and don't display the color bar or the orientation axes.
+          Export the view to "export-gltf/results/{agent_mode}/ExportedGLTF.gltf".
+
+          Next load the file "export-gltf/results/{agent_mode}/ExportedGLTF.gltf" and display it as a surface.
+          Color this object by TEXCOORD_0.
+          Scale the color map to the data, and don't display the color bar or the orientation axes.
+          Use the 'Cool to Warm' colormap.
+
+          Save a screenshot to the file "export-gltf/results/{agent_mode}/export-gltf.png".
+          Finally, save the ParaView state as "export-gltf/results/{agent_mode}/export-gltf.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. GLTF Export Quality: Is the wavelet object properly exported to GLTF format with correct surface representation and RTData coloring?
+
+          2. GLTF Import and Display: Is the exported GLTF file successfully loaded and displayed as a surface with proper geometry?
+
+          3. Texture Coordinate Coloring: Is the imported GLTF object correctly colored by TEXCOORD_0 with Cool to Warm colormap?
+
+          4. Clean Presentation: Are the color bar and orientation axes properly hidden for a clean visualization appearance?
+
+# 13. import-gltf
+- vars:
+    question: |
+          Load the "BlueGrayBackground" palette.
+          Read the file "import-gltf/data/import-gltf.glb" and import the nodes "/assembly/Axle", "assembly/OuterRing/Torus002", and "assembly/OuterRing/MiddleRing/InnerRing".
+          Set the layout size to 300x300 pixels.
+          Point the camera in the positive Y direction and zoom to fit.
+          Make sure all views are rendered, then save a screenshot to "import-gltf/results/{agent_mode}/import-gltf.png".
+          Finally, save the ParaView state as "import-gltf/results/{agent_mode}/import-gltf.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. GLTF Import Success: Are the specified GLTF nodes properly imported and displayed as separate geometric components?
+
+          2. Node Selection: Are all three specified nodes (Axle, Torus002, InnerRing) correctly imported and visible?
+
+          3. Camera Positioning: Is the camera positioned in the positive Y direction with appropriate zoom to fit all imported geometry?
+
+          4. Layout Configuration: Is the view properly sized to 300x300 pixels with correct rendering and background palette?
+
+# 14. render-histogram
+- vars:
+    question: |
+          Create a wavelet object.
+          Render the RTDATA data in the wavelet and show the color bar.
+          [optional: Make sure the colors are rescaled to the data range]
+          [optional: Use the color map called 'Cool to Warm']
+
+          Next, split the view to the right and create a histogram from RTDATA.
+          Use the same color map as before.
+          Save a screenshot of the line chart in the file "render-histogram/results/{agent_mode}/render-histogram.png".
+          Finally, save the ParaView state as "render-histogram/results/{agent_mode}/render-histogram.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Wavelet Visualization: Is the wavelet object properly rendered with RTDATA coloring and visible color bar?
+
+          2. Split View Layout: Is the view correctly split with the wavelet visualization on the left and histogram on the right?
+
+          3. Histogram Generation: Is the histogram properly generated from RTDATA showing the data distribution?
+
+          4. Color Map Consistency: Are both the wavelet visualization and histogram using the same Cool to Warm color map?
+
+# 15. reset-camera-direction
+- vars:
+    question: |
+          Create a Wavelet object, set its representation to "Surface with Edges", and set the camera direction to [0.5, 1, 0.5].
+          Save a screenshot to the file "reset-camera-direction/results/{agent_mode}/reset-camera-direction.png".
+          Finally, save the ParaView state as "reset-camera-direction/results/{agent_mode}/reset-camera-direction.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Wavelet Creation: Is the Wavelet object properly created and displayed in the scene?
+
+          2. Surface with Edges Representation: Is the wavelet correctly displayed with "Surface with Edges" representation showing both surface and wireframe?
+
+          3. Camera Direction: Is the camera positioned according to the specified direction vector [0.5, 1, 0.5]?
+
+          4. View Quality: Does the visualization provide a clear view of the wavelet structure from the specified camera angle?
+
+# 16. save-transparent
+- vars:
+    question: |
+          Create a cone object.
+          Set the transparency of the cone to be 50%.
+          Save a screenshot with a transparent background in "save-transparent/results/{agent_mode}/save-transparent.png".
+          Finally, save the ParaView state as "save-transparent/results/{agent_mode}/save-transparent.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Cone Object Creation: Is the cone object properly created and displayed in the scene?
+
+          2. Transparency Setting: Is the cone transparency correctly set to 50% showing partial see-through effect?
+
+          3. Transparent Background: Is the screenshot saved with a properly transparent background instead of solid color?
+
+          4. Visual Quality: Does the transparent cone maintain good visual quality and edge definition?
+
+# 17. subseries-of-time-series
+- vars:
+    question: |
+          Read the file "subseries-of-time-series/data/subseries-of-time-series.ex2". Load two element blocks: the first is called 'Unnamed block ID: 1 Type: HEX', the second is called 'Unnamed block ID: 2 Type: HEX'.
+          Next, slice this object with a plane with origin at [0.21706008911132812, 4.0, -5.110947132110596] and normal direction [1.0, 0.0, 0.0]. The plane should have no offset.
+          Next, save this time series to a collection of .vtm files. The base file name for the time series is "subseries-of-time-series/results/{agent_mode}/canslices.vtm" and the suffix is '_%d'. Only save time steps with index between 10 and 20 inclusive, counting by 3.
+          Next, load the files "subseries-of-time-series/results/{agent_mode}/canslices_10.vtm", "subseries-of-time-series/results/{agent_mode}/canslices_13.vtm", "subseries-of-time-series/results/{agent_mode}/canslices_16.vtm", and "subseries-of-time-series/results/{agent_mode}/canslices_19.vtm" in multi-block format.
+          Finally, show the multi-block data set you just loaded.
+          Save a screenshot to the file "subseries-of-time-series/results/{agent_mode}/subseries-of-time-series.png".
+          Finally, save the ParaView state as "subseries-of-time-series/results/{agent_mode}/subseries-of-time-series.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Data Loading and Block Selection: Are the specified element blocks properly loaded and the slice plane correctly applied?
+
+          2. Time Series Export: Is the time series correctly saved as VTM files with the specified time step range and interval?
+
+          3. Multi-block Loading: Are the exported VTM files successfully loaded back as a multi-block dataset?
+
+          4. Final Visualization: Is the multi-block dataset properly displayed showing the sliced geometry from the time series?
+
+# 18. write-ply
+- vars:
+    question: |
+          Create a cube object.
+          Export the cube to a PLY file named "write-ply/results/{agent_mode}/cube.ply".
+          Load the PLY file back into ParaView.
+          Save a screenshot to "write-ply/results/{agent_mode}/write-ply.png".
+          Finally, save the ParaView state as "write-ply/results/{agent_mode}/write-ply.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Cube Creation: Is the cube object properly created and displayed with correct geometry?
+
+          2. PLY Export: Is the cube successfully exported to PLY format with proper mesh data preservation?
+
+          3. PLY Import: Is the exported PLY file correctly loaded back into ParaView maintaining geometric fidelity?
+
+          4. Visualization Quality: Does the imported cube display properly with correct surface representation and rendering?
+
+# 19. climate
+- vars:
+    question: |
+          Read in the file named "climate/data/climate.vtp".
+          Apply a calculator filter to convert velocity from geospatial to lat-long coordinates.
+          Render the computed values using a tube filter with 0.05 radius, colored by velocity magnitude, and lit with maximum shininess and include normals for lighting.
+          Add cone glyphs to show the direction of the velocity, using 10 polygons, radius 0.15, height 0.5, and scaling factor 0.5.
+          View the result in the -z direction scaled so that the tubes occupy most of the image.
+          Save a screenshot of the result, 2294 x 1440 pixels, white background, in the filename "climate/results/{agent_mode}/climate.png".
+          Finally, save the ParaView state as "climate/results/{agent_mode}/climate.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Velocity Conversion: Is the calculator filter properly applied to convert velocity from geospatial to lat-long coordinates?
+
+          2. Tube Visualization: Are the tubes rendered with correct radius (0.05), colored by velocity magnitude, and proper lighting with maximum shininess?
+
+          3. Cone Glyph Direction: Are the cone glyphs properly configured with specified parameters and showing velocity direction accurately?
+
+          4. View Configuration: Is the visualization displayed from -z direction with appropriate scaling and white background as specified?
+
+# 20. materials
+- vars:
+    question: |
+          Compare two datasets in two views side by side each 900 pixels wide x 1400 pixels high.
+          Read the dataset "materials/data/materials_prediction.vtr" in the left view and "materials/data/materials_ground_truth.vtr" in the right view.
+          In both views, convert the "Intensity" and "Phase" variables from cell to point data.
+          In both views, take an isovolume of the "Intensity" variable in the range of [0.2, 1.0], clipped with a plane at (32.0, 32.0, 32.0) and +x normal direction.
+          Color both views with the Viridis (matplotlib) color map for the "Phase" variable, scaled to the data range, including a colormap legend in both views.
+          Label the left view "NN Prediction" and the right view "Ground Truth".
+          Orient the camera to look in the (-1, 0, -1) direction, with the datasets fitting in the views.
+          Save a screenshot of both views in "materials/results/{agent_mode}/materials.png".
+          Finally, save the ParaView state as "materials/results/{agent_mode}/materials.pvsm"
+
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Side-by-Side Comparison: Are both datasets properly displayed in side-by-side views with correct dimensions and labeling?
+
+          2. Data Conversion and Filtering: Are the Intensity and Phase variables correctly converted to point data and isovolume filtering applied?
+
+          3. Clipping and Color Mapping: Is the plane clipping correctly applied and Viridis colormap properly used for Phase variable?
+
+          4. Camera and Layout: Is the camera positioned correctly in (-1, 0, -1) direction with appropriate fitting and legends visible?

eval_cases/paraview/main_cases.yaml

@@ -0,0 +1,542 @@
+# Comprehensive Test Cases for SciVisAgentBench Main Tasks
+# This test evaluates the ability to complete specific visualization tasks
+# with detailed requirements and evaluation criteria
+
+# 1. Bonsai Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the bonsai dataset from "bonsai/data/bonsai_256x256x256_uint8.raw", the information about this dataset:
+        Bonsai (Scalar)
+        Data Scalar Type: unsigned char
+        Data Byte Order: little Endian
+        Data Spacing: 1x1x1
+        Data Extent: 256x256x256
+
+        Then visualize it with volume rendering, modify the transfer function and reach the visualization goal as: "A potted tree with brown pot silver branch and golden leaves."
+
+        Please think step by step and make sure to fulfill all the visualization goals mentioned above.
+
+        Finally, save the paraview state as "bonsai/results/{agent_mode}/bonsai.pvsm"
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Brown Pot Visualization: Does the result show the pot portion in brown color?
+
+          2. Silver Branch Visualization: Does the result show the branch/trunk portion in silver color?
+
+          3. Golden Leaves Visualization: Does the result show the leaves portion in golden color?
+
+# 2. Carp Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the carp dataset from "carp/data/carp_256x256x512_uint16.raw", the information about this dataset:
+        Carp (Scalar)
+        Data Scalar Type: unsigned short
+        Data Byte Order: little Endian
+        Data Spacing: 0.78125x0.390625x1
+        Data Extent: 256x256x512
+
+        Instructions:
+
+        1. Load the dataset into ParaView.
+
+        2. Apply volume rendering to visualize the carp skeleton.
+
+        3. Adjust the transfer function to highlight only the bony structures in an X-ray style (suppressing soft tissue).
+
+        4. Optimize the viewpoint to display the full skeleton, ensuring the head, spine, and fins are all clearly visible in a single frame.
+
+        5. Analyze the visualization and answer the following questions:
+
+        Q1: Which of the following options correctly describes the fins visible in the carp skeleton visualization?
+        A. 5 fins: 1 dorsal, 2 pectoral, 2 pelvic
+        B. 6 fins: 1 dorsal, 2 pectoral, 2 pelvic, 1 caudal
+        C. 7 fins: 1 dorsal, 2 pectoral, 2 pelvic, 1 anal, 1 caudal
+        D. 8 fins: 2 dorsal, 2 pectoral, 2 pelvic, 1 anal, 1 caudal
+
+        Q2: Based on the visualization, what is the approximate ratio of skull length to total body length?
+        A. ~15%
+        B. ~22%
+        C. ~30%
+        D. ~40%
+
+        6. Save your work:
+        Save the ParaView state as "carp/results/{agent_mode}/carp.pvsm".
+        Save the answers to the analysis questions in plain text as "carp/results/{agent_mode}/answers.txt".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Bone Isolation: Are the bones clearly visible while soft tissue and background are suppressed? Thin fin rays should be distinguishable without major loss.
+
+          2. Viewpoint Selection: Does the chosen viewpoint display the entire carp skeleton (head, spine, ribs, fins, tail) without critical occlusion?
+
+          3. X-ray Appearance: Does the visualization resemble an X-ray (monochrome or grayscale, transparent look, consistent lighting)?
+
+          4. Correct Data Setup: Was the dataset loaded with proper spacing (0.78125x0.390625x1.0)? The carp skeleton should appear in its correct proportions without distortion (i.e., the fish shape looks anatomically normal).
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: C. 7 fins: 1 dorsal, 2 pectoral, 2 pelvic, 1 anal, 1 caudal
+
+          2. Q2 correct answer: B. ~22%
+
+# 3. Chameleon Dataset (VolVis)
+- vars:
+    question: |
+        Task:
+
+        Load the chameleon dataset from "chameleon_volvis/data/chameleon_volvis_256x256x270_float32.raw", the information about this dataset:
+        chameleon (Scalar)
+        Data Scalar Type: float
+        Data Byte Order: little Endian
+        Data Extent: 256x256x270
+        Number of Scalar Components: 1
+        Data loading is very important, make sure you correctly load the dataset according to their features.
+
+        Apply the volume rendering to visualize the chameleon dataset
+
+        Adjust the transfer function to highlight the bony structures and skin in an X-ray style.
+
+        Adjust the camera position and focus on the head part of the chameleon
+
+        Please think step by step and make sure to fulfill all the visualization goals mentioned above.
+
+        Finally, save the paraview state as "chameleon_volvis/results/{agent_mode}/chameleon_volvis.pvsm"
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Visualization Goal: Does the result present a clean, X-ray–style volume rendering where the chameleon's bony structures are clearly emphasized and soft tissue is faint but discernible?
+
+          2. Data Loading Correctness: Is the RAW volume loaded with the specified metadata (float32, little-endian, 256×256×270, 1 component) so that the histogram looks reasonable and the anatomy is not flipped or distorted?
+
+          3. Transfer Function Quality: Does the grayscale transfer function make low-intensity tissue mostly transparent while assigning higher opacity to bones/skin ridges, yielding good depth cues without over-saturation or banding?
+
+          4. Camera & Framing: Is the camera positioned and zoomed to focus on the chameleon's head, keeping it sharply framed (no clipping), with a stable viewpoint that highlights key anatomical details?
+
+# 4. Engine Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the vortex dataset from "engine/data/engine_256x256x128_uint8.raw", the information about this dataset:
+        engine (Scalar)
+        Data Scalar Type: float
+        Data Byte Order: little Endian
+        Data Extent: 256x256x128
+        Number of Scalar Components: 1
+
+        Instructions:
+
+        1. Load the dataset into ParaView.
+
+        2. Apply the volume rendering to visualize the engine dataset
+
+        3. Adjust the transfer function, let the outer part more transparent and the inner part more solid. Use light blue for the outer part and orange for the inner part.
+
+        4. Save your work:
+        Save the ParaView state as "engine/results/{agent_mode}/engine.pvsm".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Visualization Goal: How well does the result use volume rendering to clearly present the internal and external structures of the engine dataset?
+
+          2. Structural Clarity: Does the visualization emphasize depth so that the outer layers do not obscure the inner structures?
+
+          3. Transfer Function Transparency: Is the outer region rendered with higher transparency and the inner region more solid, achieving a clear layering effect?
+
+          4. Transfer Function Color Mapping: Are colors correctly assigned so that the outer part is light blue and the inner part is orange, enhancing structural contrast?
+
+# 5. Solar Plume Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the tornado dataset from "solar-plume/data/solar-plume_126x126x512_float32_scalar3.raw", the information about this dataset:
+        solar-plume (Vector)
+        Data Scalar Type: float
+        Data Byte Order: little Endian
+        Data Extent: 126x126x512
+        Number of Scalar Components: 3
+        Data loading is very important, make sure you correctly load the dataset according to their features.
+
+        Add a "stream tracer" filter under the tornado data to display streamline, set the "Seed type" to "Point Cloud" and set the center of point cloud to 3D position [50, 50, 320] with a radius 30, then hide the point cloud sphere.
+
+        Add a "tube" filter under the "stream tracer" filter to enhance the streamline visualization. Set the radius to 0.5. In the pipeline browser panel, hide everything except the "tube" filter. 
+
+
+        Please think step by step and make sure to fulfill all the visualization goals mentioned above.
+
+        Finally, save the paraview state as "solar-plume/results/{agent_mode}/solar-plume.pvsm"
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Visualization Goal: How well does the result achieve the overall goal of showing tornado flow patterns with glyphs and streamlines?
+
+          2. Glyph Visualization: Does the result show velocity glyphs that are appropriately sized and visible?
+
+          3. Streamline Visualization: Does the result show streamlines that follow the flow patterns effectively?
+
+          4. Tube Rendering: Are the streamlines rendered as tubes with appropriate thickness?
+
+# 6. Supernova Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the supernova dataset from "supernova/data/supernova_256x256x256_float32.raw", the information about this dataset:
+        Supernova (Scalar)
+        Data Scalar Type: float
+        Data Byte Order: little Endian
+        Data Spacing: 1x1x1
+        Data Extent: 256x256x256
+        Data loading is very important, make sure you correctly load the dataset according to their features.
+
+        Then visualize it and extract two isosurfaces. One of them use color red, showing areas with low density (isovalue 40 and opacity 0.4), while the other use color blue, showing areas with high density (isovalue 150 and opacity 0.8).
+
+        Please think step by step and make sure to fulfill all the visualization goals mentioned above. Only make the two isosurfaces visible.
+
+        Finally, save the paraview state as "supernova/results/{agent_mode}/supernova.pvsm"
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Visualization Goal: How well does the result achieve the overall goal of showing the supernova structure with two distinct isosurfaces representing different density regions?
+
+          2. Does the red isosurface show low density areas (outside regions) with lower opacity?
+
+          3. Does the blue isosurface show high density areas (inside regions) with higher opacity?
+
+# 7. Tangaroa Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the tangaroa dataset from "tangaroa_300x180x120_float32_scalar3.raw", the information about this dataset:
+        tangaroa (Vector)
+        Data Scalar Type: float
+        Data Byte Order: little Endian
+        Data Extent: 300x180x120
+        Number of Scalar Components: 3
+        Data loading is very important, make sure you correctly load the dataset according to their features.
+
+        Apply "streamline tracer" filter, set the "Seed Type" to point cloud, turn off the "show sphere", set the center to [81.6814, 80.708, 23.5093], and radius to 29.9
+
+        Add "Ribbon" filter to the streamline tracer results and set width to 0.3, set the Display representation to Surface.
+
+        In pipeline browser panel, hide everything except the ribbon filter results.
+
+        Please think step by step and make sure to fulfill all the visualization goals mentioned above.
+
+        Finally, save the paraview state as "tangaroa/results/{agent_mode}/tangaroa.pvsm"
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Visualization Goal: How well does the result reveal the tangaroa flow structures using streamlines expanded into surfaces with the Ribbon filter?
+
+          2. Streamline Seeding: Are streamlines correctly seeded from a Point Cloud centered at [81.6814, 80.708, 23.5093] with radius 29.9, and is the seed sphere hidden?
+
+          3. Ribbon Visualization: Are the streamlines rendered with the Ribbon filter, set to width 0.3, with Display representation as Surface, effectively showing flow surfaces?
+
+# 8. Tornado Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the tornado dataset from "tornado/data/tornado_64x64x64_float32_scalar3.raw", the information about this dataset:
+        Tornado (Vector)
+        Data Scalar Type: float
+        Data Byte Order: little Endian
+        Data Extent: 64x64x64
+        Number of Scalar Components: 3
+        Data loading is very important, make sure you correctly load the dataset according to their features.
+
+        Add a "glyph" filter under the tornado data to display velocity glyph, set an appropriate "Scale Factor" so the glyphs are visible.
+
+        Then add a "stream tracer" filter under the tornado data to generate streamlines. Choose "Point Cloud" as "Seed Type", and do not show sphere.
+
+        Add a "tube" filter under the stream tracer you just created to generate tubes for visualizing the streamlines. Set an appropriate radius. Make the stream tracer invisible and the tube visible. At last, render the streamlines as tubes.
+
+        Please think step by step and make sure to fulfill all the visualization goals mentioned above.
+
+        Finally, save the paraview state as "tornado/results/{agent_mode}/tornado.pvsm"
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Visualization Goal: How well does the result achieve the overall goal of showing tornado flow patterns with glyphs and streamlines?
+
+          2. Glyph Visualization: Does the result show velocity glyphs that are appropriately sized and visible?
+
+          3. Streamline Visualization: Does the result show streamlines that follow the flow patterns effectively?
+
+          4. Tube Rendering: Are the streamlines rendered as tubes with appropriate thickness?
+
+# 9. Vortex Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the vortex dataset from "vortex/data/vortex_128x128x128_float32.raw", the information about this dataset:
+        vortex (Scalar)
+        Data Scalar Type: float
+        Data Byte Order: little Endian
+        Data Extent: 128x128x128
+        Number of Scalar Components: 1
+
+        Instructions:
+
+        1. Load the dataset into ParaView.
+
+        2. Leverage "contour" filter to achieve iso-surface rendering. In pipeline browser panel, hide everything except the "contour" fileter.
+
+        3. In properties panel of "contour" filter, set isosurface value to -0.2, use Solid Color and set the color as beige.
+
+        4. Enable Ambient occlusion by toggle the "Use Ambient Occlusion" button in the Render Passes.
+
+        5. Add head light with light inspector, set "Coords" as Camera, "Intentsity" to 0.2, Type to "Directional".
+
+        6. Save your work:
+        Save the ParaView state as "vortex/results/{agent_mode}/vortex.pvsm".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Visualization Goal: How well does the result present a clear iso-surface rendering of the vortex scalar field at value −0.2?
+
+          2. Contour Appearance: Is the contour rendered with Solid Color set to beige and made the only visible object in the pipeline?
+
+          3. Lighting & Shading: Are Ambient Occlusion and a directional head light (Coords = Camera, Intensity = 0.2) applied?
+
+# 10. Foot Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the Foot dataset from "foot/data/foot_256x256x256_uint8.raw", the information about this dataset:
+        Foot
+        Description: Rotational C-arm x-ray scan of a human foot. Tissue and bone are present in the dataset.
+        Data Type: uint8
+        Data Byte Order: little Endian
+        Data Spacing: 1x1x1
+        Data Extent: 256x256x256
+        Data loading is very important, make sure you correctly load the dataset according to their features.
+
+        Visualize the anatomical structures:
+        1. Apply volume rendering with an X-ray transfer function that distinguishes soft tissues and bones. Bones with darker color, and soft tissue with lighter color.
+
+        2. Analyze the visualization and answer the following questions:
+
+        Q1: Based on the X-ray style volume rendering of the foot dataset, which of the following best describes the visibility of bony structures?
+        A. Both the phalanges and metatarsals are fully visible
+        B. The phalanges are fully visible, but the metatarsals are only partially visible
+        C. The metatarsals are fully visible, but the phalanges are only partially visible
+        D. Neither the phalanges nor the metatarsals are clearly visible
+
+        3. Save your work:
+        Save the ParaView state as "foot/results/{agent_mode}/foot.pvsm".
+        Save the answers to the analysis questions in plain text as "foot/results/{agent_mode}/answers.txt".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Goal: Does the visualization effectively distinguish between different tissue types in the foot dataset?
+
+          2. X-ray Appearance: Does the visualization resemble an X-ray (monochrome or grayscale, transparent look, consistent lighting)?
+
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: B. The phalanges are fully visible, but the metatarsals are only partially visible
+
+# 11. Lobster Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the Lobster dataset from "lobster/data/lobster_301x324x56_uint8.raw", the information about this dataset:
+        Lobster
+        Description: CT scan of a lobster contained in a block of resin.
+        Data Type: uint8
+        Data Byte Order: little Endian
+        Data Spacing: 1x1x1.4
+        Data Extent: 301x324x56
+        Data loading is very important, make sure you correctly load the dataset according to their features.
+
+        Visualize the scanned specimen:
+        1. Create an isosurface at the specimen boundary, find a proper isovalue to show the whole structure.
+
+        2. Use natural colors appropriate for the specimen (red-orange for lobster)
+
+        3. Analyze the visualization and answer the following questions:
+
+        Q1: Based on the isosurface visualization of the lobster specimen, how many walking legs are visible?
+        A. 6 walking legs
+        B. 7 walking legs
+        C. 8 walking legs
+        D. 10 walking legs
+
+        4. Save your work:
+        Save the ParaView state as "lobster/results/{agent_mode}/lobster.pvsm".
+        Save the answers to the analysis questions in plain text as "lobster/results/{agent_mode}/answers.txt".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Goal: Does the visualization clearly show the structure and details of the Lobster?
+
+          2. Boundary Clearity: Are surface details and boundaries of the lobster well-defined?
+
+          3. Correct Color: Is the color of the lobster mimic a real one? (red-orange)
+
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: B. 7 walking legs
+
+# 12. Chameleon Dataset (IsoSurface)
+- vars:
+    question: |
+        Task:
+        Load the chameleon dataset from "chameleon_isosurface/data/chameleon_isosurface_256x256x256_float32.vtk".
+        Generate a visualization image of 2 isosurfaces of the Chameleon scalar field dataset with the following visualization settings:
+        1) Create isosurfaces of Iso_1 with a value of 0.12 and Iso_2 with a value of 0.45
+        2) Assign RGB color of [0.0, 1.0, 0.0] to Iso_1, and color of [1.0, 1.0, 1.0] to Iso_2
+        3) Assign opacity of 0.1 to Iso_1, and opacity of 0.99 to Iso_2
+        4) Set the lighting parameter as: 0.1 to Ambient; 0.7 to Diffuse; 0.6 to Specular
+        5) Set the viewpoint parameters as: [600, 0, 0] to position; [0, 0, 0] to focal point; [0, -1, 0] to camera up direction
+        6) White background
+        7) Visualization image resolution is 1024x1024
+        8) Save the visualization image as a png file "chameleon_isosurface/results/{agent_mode}/chameleon_isosurface.png"
+        9) (Option 1) Save the paraview state as "chameleon_isosurface/results/{agent_mode}/chameleon_isosurface.pvsm" if you are using ParaView as the visualization tool
+        10) (Option 2) Save the cxx code script as "chameleon_isosurface/results/{agent_mode}/chameleon_isosurface.cxx" if you are using VTK as the visualization tool
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Overall Visualization Goal: Does the result present a good isosurface rendering compared to groundtruth?
+          
+          2. Is the skin of the Chameleon object of green color?
+          
+          3. Is the bone of the Chameleon object of white color?
+
+
+# 13. Argon Bubble
+# A CFD simulation of a bubble of argon gas immersed in air and being hit by a shockwave. 
+# This dataset is a time-varying volume dataset created by the Center for Computational Sciences and Engineering (CCSE) at Lawrence Berkeley National Laboratory.
+# The volumetric used for the SciVis benchmark is one frame of the time sequence.
+- vars:
+    question: |
+        Task:
+        Load the Argon Bubble dataset from "argon-bubble/data/argon-bubble_128x128x256_float32.vtk".
+        Generate a visualization image of the Argon Bubble scalar field dataset with the following visualization settings:
+        1) Create volume rendering
+        2) Set the opacity transfer function as a ramp function across values of the volumetric data, assigning opacity 0 to value 0 and assigning opacity 1 to value 1.
+        3) Set the color transfer function to assign a warm red color [0.71, 0.02, 0.15] to the highest value, a cool color [0.23, 0.29, 0.75] to the lowest value, and a grey color[0.87, 0.87, 0.87] to the midrange value
+        4) Set the viewpoint parameters as: [0, 450, 0] to position; [0, 0, -15] to focal point; [0, 0, -1] to camera up direction
+        5) Visualization image resolution is 1024x1024. White background. Shade turned off. Volume rendering ray casting sample distance is 0.1
+        6) Save the visualization image as a png file "argon-bubble/results/{agent_mode}/argon-bubble.png"
+        7) (Option 1) Save the paraview state as "argon-bubble/results/{agent_mode}/argon-bubble.pvsm" if you are using ParaView as the visualization tool
+        8) (Option 2) Save the cxx code script as "argon-bubble/results/{agent_mode}/argon-bubble.cxx" if you are using VTK as the visualization tool
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the visualization image clearly show the regions of cool, warm, and mild regions?
+
+          2. Does the blueish region show areas with low opacity?
+
+          3. Does the reddish region show areas with high opacity?
+
+
+# 14. Richtmyer-Meshkov Instability Simulation
+# Entropy field (timestep 160) of Richtmyer-Meshkov instability simulation
+- vars:
+    question: |
+        Task:
+        Load the Richtmyer dataset from "richtmyer/data/richtmyer_256x256x240_float32.vtk".
+        Generate a visualization image of the Richtmyer dataset, Entropy field (timestep 160) of Richtmyer-Meshkov instability simulation, with the following visualization settings: 
+        1) Create volume rendering
+        2) Set the opacity transfer function as a ramp function from value 0.05 to 1 of the volumetric data, assigning opacity 0 to value less than 0.05 and assigning opacity 1 to value 1.
+        3) Set the color transfer function following the 7 rainbow colors and assign a red color [1.0, 0.0, 0.0] to the highest value, a purple color [0.5, 0.0, 1.0] to the lowest value.
+        4) Visualization image resolution is 1024x1024
+        5) Set the viewpoint parameters as: [420, 420, -550] to position; [128, 128, 150] to focal point; [-1, -1, 1] to camera up direction
+        6) Turn on the shade and set the ambient, diffuse and specular as 1.0
+        7) White background. Volume rendering ray casting sample distance is 0.1
+        8) Save the visualization image as a png file "richtmyer/results/{agent_mode}/richtmyer.png"
+        9) (Option 1) Save the paraview state as "richtmyer/results/{agent_mode}/richtmyer.pvsm" if you are using ParaView as the visualization tool
+        10) (Option 2) Save the cxx code script as "richtmyer/results/{agent_mode}/richtmyer.cxx" if you are using VTK as the visualization tool
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the visualization show a clear surface with peaks and valleys?
+
+          2. Are the peaks highlighted with the color yellow?
+
+          3. Are the valleys highlighted with the color blue?
+
+
+# 15. Rayleigh-Taylor Instability (Miranda)
+# A time step of a density field in a simulation of the mixing transition in Rayleigh-Taylor instability
+- vars:
+    question: |
+        Task:
+        Load the Rayleigh-Taylor Instability dataset from "miranda/data/miranda_256x256x256_float32.vtk".
+        Generate a visualization image of the Rayleigh-Taylor Instability dataset, a time step of a density field in a simulation of the mixing transition in Rayleigh-Taylor instability, with the following visualization settings:
+        1) Create volume rendering
+        2) Set the opacity transfer function as a ramp function from value 0 to 1 of the volumetric data, assigning opacity 0 to value 0 and assigning opacity 1 to value 1.
+        3) Set the color transfer function following the 7 rainbow colors and assign a red color [1.0, 0.0, 0.0] to the highest value, a purple color [0.5, 0.0, 1.0] to the lowest value.
+        4) Set the viewpoint parameters as: [650, 650, 650] to position; [128, 128, 128] to focal point; [1, 0, 0] to camera up direction
+        5) Volume rendering ray casting sample distance is 0.1
+        6) White background
+        7) Visualization image resolution is 1024x1024
+        8) Save the visualization image as a png file "miranda/results/{agent_mode}/miranda.png"
+        9) (Option 1) Save the paraview state as "miranda/results/{agent_mode}/miranda.pvsm" if you are using ParaView as the visualization tool
+        10) (Option 2) Save the cxx code script as "miranda/results/{agent_mode}/miranda.cxx" if you are using VTK as the visualization tool
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the visualization image clearly show the regions from low to high intensity?
+
+          2. Does the purple region show areas with low opacity?
+
+          3. Does the red region show areas with high opacity?
+
+
+# 16. Rotstrat
+# Temperature field of a direct numerical simulation of rotating stratified turbulence
+- vars:
+    question: |
+        Task:
+        Load the rotstrat dataset from "rotstrat/data/rotstrat_256x256x256_float32.vtk".
+        Generate a visualization image of the Rotstrat dataset, temperature field of a direct numerical simulation of rotating stratified turbulence, with the following visualization settings: 
+        1) Create volume rendering
+        2) Set the opacity transfer function as a step function jumping from 0 to 1 at value 0.12
+        3) Set the color transfer function to assign a warm red color [0.71, 0.02, 0.15] to the highest value, a cool color [0.23, 0.29, 0.75] to the lowest value, and a grey color[0.87, 0.87, 0.87] to the midrange value
+        4) Set the viewpoint parameters as: [800, 128, 128] to position; [0, 128, 128] to focal point; [0, 1, 0] to camera up direction
+        5) Volume rendering ray casting sample distance is 0.1
+        6) White background
+        7) Visualization image resolution is 1024x1024
+        8) Save the visualization image as a png file "rotstrat/results/{agent_mode}/rotstrat.png"
+        9) (Option 1) Save the paraview state as "rotstrat/results/{agent_mode}/rotstrat.pvsm" if you are using ParaView as the visualization tool
+        10) (Option 2) Save the cxx code script as "rotstrat/results/{agent_mode}/rotstrat.cxx" if you are using VTK as the visualization tool
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Does the visualization image clearly show the shape of turbulence compared to ground truth?
+
+          2. Does the blueish region show areas with low opacity?
+
+          3. Does the reddish region show areas with high opacity?

eval_cases/paraview/what_obj_cases.yaml

@@ -0,0 +1,526 @@
+# Comprehensive Data Identification Test Cases for SciVisAgentBench
+# This test evaluates the ability to identify and understand data content
+# without prior knowledge from metadata or naming patterns
+
+# 1. Aneurism Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/aneurism/data/aneurism_256x256x256_uint8.raw".
+        Use visualization tools to determine what object or structure is contained in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/aneurism/results/{agent_mode}/aneurism.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/aneurism/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          The assistant should identify the data shows an aneurism or vascular structure
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          The assistant should identify the data shows an aneurism or vascular structure
+
+# # 2. Backpack Dataset
+# - vars:
+#     question: |
+#         Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/backpack/data/backpack_512x512x373_uint16.raw".
+#         Use visualization tools to determine what object is contained in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/backpack/results/{agent_mode}/backpack.pvsm"
+#         Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/backpack/results/{agent_mode}/answers.txt"
+#   assert:
+#     - type: llm-rubric
+#       subtype: text
+#       value: |
+#           The assistant should identify that the data shows a backpack
+#     - type: llm-rubric
+#       subtype: vision
+#       value: |
+#           The assistant should identify that the data shows a backpack
+
+# 3. Blunt Fin Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/blunt_fin/data/blunt_fin_256x128x64_uint8.raw".
+        Use visualization tools to determine what object or structure is in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/blunt_fin/results/{agent_mode}/blunt_fin.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/blunt_fin/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          The assistant should identify a fin or aerodynamic strcuture or simulation result in the data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          The assistant should identify a fin or aerodynamic strcuture or simulation result in the data
+
+# 4. Bonsai Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/bonsai/data/bonsai_256x256x256_uint8.raw".
+        Use visualization tools to determine what object is contained in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/bonsai/results/{agent_mode}/bonsai.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/bonsai/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a bonsai tree or botanical structure in the data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a bonsai tree or botanical structure in the data
+
+# 5. Boston Teapot Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/boston_teapot/data/boston_teapot_256x256x178_uint8.raw".
+        Use visualization tools to determine what object is in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/boston_teapot/results/{agent_mode}/boston_teapot.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/boston_teapot/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a teapot in the visualization
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a teapot in the visualization
+
+# 6. Bunny Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/bunny/data/bunny_512x512x361_uint16.raw".
+        Use visualization tools to determine what object is in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/bunny/results/{agent_mode}/bunny.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/bunny/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a bunny or rabbit in the 3D scanned data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a bunny or rabbit in the 3D scanned data
+
+# 7. Carp Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/carp/data/carp_256x256x512_uint16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/carp/results/{agent_mode}/carp.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/carp/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a carp or fish anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a carp or fish anatomy
+
+# 8. CSAFE Heptane Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/csafe_heptane/data/csafe_heptane_302x302x302_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/csafe_heptane/results/{agent_mode}/csafe_heptane.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/csafe_heptane/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should recognize combustion or heptane simulation data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should recognize combustion or heptane simulation data
+
+# 9. Duct Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/duct/data/duct_193x194x1000_float32.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/duct/results/{agent_mode}/duct.pvsm"
+        Take a screenshot and provide a textual report describing what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/duct/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify flow patterns in a duct geometry
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify flow patterns in a duct geometry
+
+# 10. Engine Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/engine/data/engine_256x256x128_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/engine/results/{agent_mode}/engine.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/engine/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify an engine or mechanical components
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify an engine or mechanical components
+
+# 11. Foot Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/foot/data/foot_256x256x256_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/foot/results/{agent_mode}/foot.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/foot/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a foot with bone and tissue structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a foot with bone and tissue structures
+
+# 12. Frog Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/frog/data/frog_256x256x44_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/frog/results/{agent_mode}/frog.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/frog/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a frog specimen with internal anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a frog specimen with internal anatomy
+
+# 13. Fuel Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/fuel/data/fuel_64x64x64_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/fuel/results/{agent_mode}/fuel.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/fuel/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify fuel combustion or related simulation
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify fuel combustion or related simulation
+
+# 14. Hydrogen Atom Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/hydrogen_atom/data/hydrogen_atom_128x128x128_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/hydrogen_atom/results/{agent_mode}/hydrogen_atom.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/hydrogen_atom/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should recognize hydrogen atom orbital or probability distribution
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should recognize hydrogen atom orbital or probability distribution
+
+# 15. Lobster Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/lobster/data/lobster_301x324x56_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/lobster/results/{agent_mode}/lobster.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/lobster/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a lobster or crustacean anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a lobster or crustacean anatomy
+
+# 16. Marschner-Lobb Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/marschner_lobb/data/marschner_lobb_41x41x41_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/marschner_lobb/results/{agent_mode}/marschner_lobb.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/marschner_lobb/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should recognize Marschner-Lobb synthetic test pattern
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should recognize Marschner-Lobb synthetic test pattern
+
+# 17. MRI Ventricles Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/mri_ventricles/data/mri_ventricles_256x256x124_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/mri_ventricles/results/{agent_mode}/mri_ventricles.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/mri_ventricles/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify brain ventricles or ventricular structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify brain ventricles or ventricular structures
+
+# 18. MRI Woman Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/mri_woman/data/mri_woman_256x256x109_uint16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/mri_woman/results/{agent_mode}/mri_woman.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/mri_woman/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify human anatomical structures from MRI scan
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify human anatomical structures from MRI scan
+
+# 19. MRT Angio Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/mrt_angio/data/mrt_angio_416x512x112_uint16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/mrt_angio/results/{agent_mode}/mrt_angio.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/mrt_angio/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify angiography or vascular structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify angiography or vascular structures
+
+# 20. Neghip Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/neghip/data/neghip_64x64x64_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/neghip/results/{agent_mode}/neghip.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/neghip/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should visualize and describe molecule structure
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should visualize and describe molecule structure
+
+# 21. Neocortical Layer 1 Axons Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/neocortical_layer_1_axons/data/neocortical_layer_1_axons_1464x1033x76_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/neocortical_layer_1_axons/results/{agent_mode}/neocortical_layer_1_axons.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/neocortical_layer_1_axons/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify neural axons or neocortical network structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify neural axons or neocortical network structures
+
+# 22. Nucleon Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/nucleon/data/nucleon_41x41x41_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/nucleon/results/{agent_mode}/nucleon.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/nucleon/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should visualize nucleon or particle physics data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should visualize nucleon or particle physics data
+
+# 23. Pancreas Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/pancreas/data/pancreas_240x512x512_int16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/pancreas/results/{agent_mode}/pancreas.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/pancreas/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify pancreas or pancreatic anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify pancreas or pancreatic anatomy
+
+# 24. Shockwave Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/shockwave/data/shockwave_64x64x512_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/shockwave/results/{agent_mode}/shockwave.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/shockwave/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify shockwave or wave propagation patterns
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify shockwave or wave propagation patterns
+
+# 25. Silicium Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/silicium/data/silicium_98x34x34_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/silicium/results/{agent_mode}/silicium.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/silicium/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify silicon crystal or material structure
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify silicon crystal or material structure
+
+# 26. Skull Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/skull/data/skull_256x256x256_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/skull/results/{agent_mode}/skull.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/skull/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Should identify skull or cranial bone structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Should identify skull or cranial bone structures
+
+# 27. Statue Leg Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/statue_leg/data/statue_leg_341x341x93_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/statue_leg/results/{agent_mode}/statue_leg.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/statue_leg/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a statue leg or sculptural form
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a statue leg or sculptural form
+
+# 28. Stent Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/stent/data/stent_512x512x174_uint16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/stent/results/{agent_mode}/stent.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/stent/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      value: |
+          Should identify a stent or medical device mesh structure
+
+# 29. Supernova Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/supernova/data/supernova_256x256x256_float32.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/supernova/results/{agent_mode}/supernova.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/supernova/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify supernova or astrophysical explosion simulation
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify supernova or astrophysical explosion simulation
+
+# 30. TACC Turbulence Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/tacc_turbulence/data/tacc_turbulence_256x256x256_float32.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/tacc_turbulence/results/{agent_mode}/tacc_turbulence.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/tacc_turbulence/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify turbulence or vortex flow structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify turbulence or vortex flow structures
+
+# 31. Tooth Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/tooth/data/tooth_103x94x161_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/tooth/results/{agent_mode}/tooth.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/tooth/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify tooth or dental anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify tooth or dental anatomy
+
+# 32. Tornado Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/tornado/data/tornado_64x64x64_float32_scalar3.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/tornado/results/{agent_mode}/tornado.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/tornado/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify tornado or vortex flow pattern
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify tornado or vortex flow pattern
+
+# 33. Visible Male Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "../SciVisAgentBench-tasks/sci_volume_data/vis_male/data/vis_male_128x256x256_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "../SciVisAgentBench-tasks/sci_volume_data/vis_male/results/{agent_mode}/vis_male.pvsm"
+        Provide a textual report identifying what you observe and save it to "../SciVisAgentBench-tasks/sci_volume_data/vis_male/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify human anatomical structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify human anatomical structures 

eval_cases/paraview/what_obj_cases_anonymized.yaml

@@ -0,0 +1,526 @@
+# Comprehensive Data Identification Test Cases for SciVisAgentBench
+# This test evaluates the ability to identify and understand data content
+# without prior knowledge from metadata or naming patterns
+
+# 1. Aneurism Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_001/data/data_001_256x256x256_uint8.raw".
+        Use visualization tools to determine what object or structure is contained in this dataset. Save the paraview state as "anonymized_datasets/dataset_001/results/{agent_mode}/dataset_001.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_001/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          The assistant should identify the data shows an aneurism or vascular structure
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          The assistant should identify the data shows an aneurism or vascular structure
+
+# # 2. Backpack Dataset
+# - vars:
+#     question: |
+#         Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_002/data/data_002_512x512x373_uint16.raw".
+#         Use visualization tools to determine what object is contained in this dataset. Save the paraview state as "anonymized_datasets/dataset_002/results/{agent_mode}/dataset_002.pvsm"
+#         Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_002/results/{agent_mode}/answers.txt"
+#   assert:
+#     - type: llm-rubric
+#       subtype: text
+#       value: |
+#           The assistant should identify that the data shows a backpack
+#     - type: llm-rubric
+#       subtype: vision
+#       value: |
+#           The assistant should identify that the data shows a backpack
+
+# 3. Blunt Fin Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_003/data/data_003_256x128x64_uint8.raw".
+        Use visualization tools to determine what object or structure is in this dataset. Save the paraview state as "anonymized_datasets/dataset_003/results/{agent_mode}/dataset_003.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_003/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          The assistant should identify a fin or aerodynamic strcuture or simulation result in the data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          The assistant should identify a fin or aerodynamic strcuture or simulation result in the data
+
+# 4. Bonsai Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_004/data/data_004_256x256x256_uint8.raw".
+        Use visualization tools to determine what object is contained in this dataset. Save the paraview state as "anonymized_datasets/dataset_004/results/{agent_mode}/dataset_004.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_004/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a bonsai tree or botanical structure in the data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a bonsai tree or botanical structure in the data
+
+# 5. Boston Teapot Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_005/data/data_005_256x256x178_uint8.raw".
+        Use visualization tools to determine what object is in this dataset. Save the paraview state as "anonymized_datasets/dataset_005/results/{agent_mode}/dataset_005.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_005/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a teapot in the visualization
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a teapot in the visualization
+
+# 6. Bunny Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_006/data/data_006_512x512x361_uint16.raw".
+        Use visualization tools to determine what object is in this dataset. Save the paraview state as "anonymized_datasets/dataset_006/results/{agent_mode}/dataset_006.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_006/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a bunny or rabbit in the 3D scanned data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a bunny or rabbit in the 3D scanned data
+
+# 7. Carp Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_007/data/carp_256x256x512_uint16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_007/results/{agent_mode}/dataset_007.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_007/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a carp or fish anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a carp or fish anatomy
+
+# 8. CSAFE Heptane Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_008/data/data_007_302x302x302_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_008/results/{agent_mode}/dataset_008.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_008/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should recognize combustion or heptane simulation data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should recognize combustion or heptane simulation data
+
+# 9. Duct Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_009/data/data_008_193x194x1000_float32.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_009/results/{agent_mode}/dataset_009.pvsm"
+        Take a screenshot and provide a textual report describing what you observe and save it to "anonymized_datasets/dataset_009/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify flow patterns in a duct geometry
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify flow patterns in a duct geometry
+
+# 10. Engine Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_010/data/data_009_256x256x128_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_010/results/{agent_mode}/dataset_010.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_010/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify an engine or mechanical components
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify an engine or mechanical components
+
+# 11. Foot Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_011/data/data_010_256x256x256_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_011/results/{agent_mode}/dataset_011.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_011/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a foot with bone and tissue structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a foot with bone and tissue structures
+
+# 12. Frog Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_012/data/data_011_256x256x44_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_012/results/{agent_mode}/dataset_012.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_012/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a frog specimen with internal anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a frog specimen with internal anatomy
+
+# 13. Fuel Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_013/data/fuel_64x64x64_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_013/results/{agent_mode}/dataset_013.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_013/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify fuel combustion or related simulation
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify fuel combustion or related simulation
+
+# 14. Hydrogen Atom Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_014/data/data_012_128x128x128_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_014/results/{agent_mode}/dataset_014.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_014/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should recognize hydrogen atom orbital or probability distribution
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should recognize hydrogen atom orbital or probability distribution
+
+# 15. Lobster Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_015/data/data_013_301x324x56_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_015/results/{agent_mode}/dataset_015.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_015/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a lobster or crustacean anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a lobster or crustacean anatomy
+
+# 16. Marschner-Lobb Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_016/data/marschner_lobb_41x41x41_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_016/results/{agent_mode}/dataset_016.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_016/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should recognize Marschner-Lobb synthetic test pattern
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should recognize Marschner-Lobb synthetic test pattern
+
+# 17. MRI Ventricles Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_017/data/data_014_256x256x124_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_017/results/{agent_mode}/dataset_017.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_017/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify brain ventricles or ventricular structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify brain ventricles or ventricular structures
+
+# 18. MRI Woman Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_018/data/data_015_256x256x109_uint16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_018/results/{agent_mode}/dataset_018.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_018/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify human anatomical structures from MRI scan
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify human anatomical structures from MRI scan
+
+# 19. MRT Angio Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_019/data/data_016_416x512x112_uint16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_019/results/{agent_mode}/dataset_019.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_019/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify angiography or vascular structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify angiography or vascular structures
+
+# 20. Neghip Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_020/data/data_017_64x64x64_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_020/results/{agent_mode}/dataset_020.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_020/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should visualize and describe molecule structure
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should visualize and describe molecule structure
+
+# 21. Neocortical Layer 1 Axons Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_021/data/neocortical_layer_1_axons_1464x1033x76_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_021/results/{agent_mode}/dataset_021.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_021/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify neural axons or neocortical network structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify neural axons or neocortical network structures
+
+# 22. Nucleon Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_022/data/data_018_41x41x41_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_022/results/{agent_mode}/dataset_022.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_022/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should visualize nucleon or particle physics data
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should visualize nucleon or particle physics data
+
+# 23. Pancreas Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_023/data/pancreas_240x512x512_int16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_023/results/{agent_mode}/dataset_023.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_023/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify pancreas or pancreatic anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify pancreas or pancreatic anatomy
+
+# 24. Shockwave Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_024/data/shockwave_64x64x512_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_024/results/{agent_mode}/dataset_024.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_024/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify shockwave or wave propagation patterns
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify shockwave or wave propagation patterns
+
+# 25. Silicium Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_025/data/silicium_98x34x34_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_025/results/{agent_mode}/dataset_025.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_025/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify silicon crystal or material structure
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify silicon crystal or material structure
+
+# 26. Skull Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_026/data/skull_256x256x256_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_026/results/{agent_mode}/dataset_026.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_026/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Should identify skull or cranial bone structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Should identify skull or cranial bone structures
+
+# 27. Statue Leg Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_027/data/data_019_341x341x93_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_027/results/{agent_mode}/dataset_027.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_027/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify a statue leg or sculptural form
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify a statue leg or sculptural form
+
+# 28. Stent Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_028/data/stent_512x512x174_uint16.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_028/results/{agent_mode}/dataset_028.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_028/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      value: |
+          Should identify a stent or medical device mesh structure
+
+# 29. Supernova Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_029/data/data_020_256x256x256_float32.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_029/results/{agent_mode}/dataset_029.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_029/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify supernova or astrophysical explosion simulation
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify supernova or astrophysical explosion simulation
+
+# 30. TACC Turbulence Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_030/data/tacc_turbulence_256x256x256_float32.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_030/results/{agent_mode}/dataset_030.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_030/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify turbulence or vortex flow structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify turbulence or vortex flow structures
+
+# 31. Tooth Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_031/data/data_021_103x94x161_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_031/results/{agent_mode}/dataset_031.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_031/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify tooth or dental anatomy
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify tooth or dental anatomy
+
+# 32. Tornado Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_032/data/data_022_64x64x64_float32_scalar3.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_032/results/{agent_mode}/dataset_032.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_032/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify tornado or vortex flow pattern
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify tornado or vortex flow pattern
+
+# 33. Visible Male Dataset
+- vars:
+    question: |
+        Clear the ParaView pipeline and load the data file "anonymized_datasets/dataset_033/data/data_023_128x256x256_uint8.raw".
+        Use visualization tools to examine what is shown in this dataset. Save the paraview state as "anonymized_datasets/dataset_033/results/{agent_mode}/dataset_033.pvsm"
+        Provide a textual report identifying what you observe and save it to "anonymized_datasets/dataset_033/results/{agent_mode}/answers.txt"
+  assert:
+    - type: llm-rubric
+      subtype: text
+      value: |
+          Should identify human anatomical structures
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          Should identify human anatomical structures 

eval_cases/topology/topology_cases.yaml

@@ -0,0 +1,89 @@
+# Test Cases for SciVisAgentBench Topology Tasks
+# This test evaluates the ability to complete specific visualization tasks
+# with detailed requirements and evaluation criteria
+
+# 1. QMCPack
+# Quantum Monte Carlo simulation of an unspecified field for an unspecified molecule. The data was taken from the 145th orbital.
+# The data was accessed from the SDR bench (note: please cite https://sdrbench.github.io/)
+# The data is released under the University of Illinois open source license.
+- vars:
+    question: |
+        1. Please load the dataset from "QMCPack/data/QMCPack.vti".
+
+        2. Compute the critical points of the scalar field.
+
+        3. Save the critical points as "QMCPack/results/{agent_mode}/QMCPack.vtk" in legacy VTK format.
+          - The output should contain the critical points as point data
+          - Include a point data array named "CriticalType" (integer) indicating the type of each critical point:
+            * 0 for minima
+            * 1 for 1-saddles
+            * 2 for 2-saddles  
+            * 3 for maxima
+            * 4 for degenerate critical points
+          - The point coordinates should be in index space (grid coordinates), not world coordinates
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Brown Pot Visualization: Does the result show the pot portion in brown color?
+
+          2. Silver Branch Visualization: Does the result show the branch/trunk portion in silver color?
+
+          3. Golden Leaves Visualization: Does the result show the leaves portion in golden color?
+
+# 2. Carp Dataset
+- vars:
+    question: |
+        Task:
+
+        Load the carp dataset from "carp/data/carp_256x256x512_uint16.raw", the information about this dataset:
+        Carp (Scalar)
+        Data Scalar Type: unsigned short
+        Data Byte Order: little Endian
+        Data Spacing: 0.78125x0.390625x1
+        Data Extent: 256x256x512
+
+        Instructions:
+
+        1. Load the dataset into ParaView.
+
+        2. Apply volume rendering to visualize the carp skeleton.
+
+        3. Adjust the transfer function to highlight only the bony structures in an X-ray style (suppressing soft tissue).
+
+        4. Optimize the viewpoint to display the full skeleton, ensuring the head, spine, and fins are all clearly visible in a single frame.
+
+        5. Analyze the visualization and answer the following questions:
+
+        Q1: Which of the following options correctly describes the fins visible in the carp skeleton visualization?
+        A. 5 fins: 1 dorsal, 2 pectoral, 2 pelvic
+        B. 6 fins: 1 dorsal, 2 pectoral, 2 pelvic, 1 caudal
+        C. 7 fins: 1 dorsal, 2 pectoral, 2 pelvic, 1 anal, 1 caudal
+        D. 8 fins: 2 dorsal, 2 pectoral, 2 pelvic, 1 anal, 1 caudal
+
+        Q2: Based on the visualization, what is the approximate ratio of skull length to total body length?
+        A. ~15%
+        B. ~22%
+        C. ~30%
+        D. ~40%
+
+        6. Save your work:
+        Save the ParaView state as "carp/results/{agent_mode}/carp.pvsm".
+        Save the answers to the analysis questions in plain text as "carp/results/{agent_mode}/answers.txt".
+  assert:
+    - type: llm-rubric
+      subtype: vision
+      value: |
+          1. Bone Isolation: Are the bones clearly visible while soft tissue and background are suppressed? Thin fin rays should be distinguishable without major loss.
+
+          2. Viewpoint Selection: Does the chosen viewpoint display the entire carp skeleton (head, spine, ribs, fins, tail) without critical occlusion?
+
+          3. X-ray Appearance: Does the visualization resemble an X-ray (monochrome or grayscale, transparent look, consistent lighting)?
+
+          4. Correct Data Setup: Was the dataset loaded with proper spacing (0.78125x0.390625x1.0)? The carp skeleton should appear in its correct proportions without distortion (i.e., the fish shape looks anatomically normal).
+    - type: llm-rubric
+      subtype: text
+      value: |
+          1. Q1 correct answer: C. 7 fins: 1 dorsal, 2 pectoral, 2 pelvic, 1 anal, 1 caudal
+
+          2. Q2 correct answer: B. ~22%

molecular_vis/workflows/curved-membrane/GS/curved-membrane_gs.vmd

@@ -0,0 +1,887 @@
+#!/usr/local/bin/vmd
+# VMD script written by save_state $Revision: 1.48 $
+# VMD version: 1.9.4a57
+set viewplist {}
+set fixedlist {}
+proc vmdrestoremymaterials {} {
+  set mlist { Opaque Transparent BrushedMetal Diffuse Ghost Glass1 Glass2 Glass3 Glossy HardPlastic MetallicPastel Steel Translucent Edgy EdgyShiny EdgyGlass Goodsell AOShiny AOChalky AOEdgy BlownGlass GlassBubble RTChrome }
+  set mymlist [material list]
+  foreach mat $mlist {
+    if { [lsearch $mymlist $mat] == -1 } { 
+      material add $mat
+    }
+  }
+  material change ambient Opaque 0.000000
+  material change diffuse Opaque 0.650000
+  material change specular Opaque 0.500000
+  material change shininess Opaque 0.534020
+  material change mirror Opaque 0.000000
+  material change opacity Opaque 1.000000
+  material change outline Opaque 0.000000
+  material change outlinewidth Opaque 0.000000
+  material change transmode Opaque 0.000000
+  material change ambient Transparent 0.000000
+  material change diffuse Transparent 0.650000
+  material change specular Transparent 0.500000
+  material change shininess Transparent 0.534020
+  material change mirror Transparent 0.000000
+  material change opacity Transparent 0.300000
+  material change outline Transparent 0.000000
+  material change outlinewidth Transparent 0.000000
+  material change transmode Transparent 0.000000
+  material change ambient BrushedMetal 0.080000
+  material change diffuse BrushedMetal 0.390000
+  material change specular BrushedMetal 0.340000
+  material change shininess BrushedMetal 0.150000
+  material change mirror BrushedMetal 0.000000
+  material change opacity BrushedMetal 1.000000
+  material change outline BrushedMetal 0.000000
+  material change outlinewidth BrushedMetal 0.000000
+  material change transmode BrushedMetal 0.000000
+  material change ambient Diffuse 0.000000
+  material change diffuse Diffuse 0.620000
+  material change specular Diffuse 0.000000
+  material change shininess Diffuse 0.530000
+  material change mirror Diffuse 0.000000
+  material change opacity Diffuse 1.000000
+  material change outline Diffuse 0.000000
+  material change outlinewidth Diffuse 0.000000
+  material change transmode Diffuse 0.000000
+  material change ambient Ghost 0.000000
+  material change diffuse Ghost 0.000000
+  material change specular Ghost 1.000000
+  material change shininess Ghost 0.230000
+  material change mirror Ghost 0.000000
+  material change opacity Ghost 0.100000
+  material change outline Ghost 0.000000
+  material change outlinewidth Ghost 0.000000
+  material change transmode Ghost 0.000000
+  material change ambient Glass1 0.000000
+  material change diffuse Glass1 0.500000
+  material change specular Glass1 0.650000
+  material change shininess Glass1 0.530000
+  material change mirror Glass1 0.000000
+  material change opacity Glass1 0.150000
+  material change outline Glass1 0.000000
+  material change outlinewidth Glass1 0.000000
+  material change transmode Glass1 0.000000
+  material change ambient Glass2 0.520000
+  material change diffuse Glass2 0.760000
+  material change specular Glass2 0.220000
+  material change shininess Glass2 0.590000
+  material change mirror Glass2 0.000000
+  material change opacity Glass2 0.680000
+  material change outline Glass2 0.000000
+  material change outlinewidth Glass2 0.000000
+  material change transmode Glass2 0.000000
+  material change ambient Glass3 0.150000
+  material change diffuse Glass3 0.250000
+  material change specular Glass3 0.750000
+  material change shininess Glass3 0.800000
+  material change mirror Glass3 0.000000
+  material change opacity Glass3 0.500000
+  material change outline Glass3 0.000000
+  material change outlinewidth Glass3 0.000000
+  material change transmode Glass3 0.000000
+  material change ambient Glossy 0.000000
+  material change diffuse Glossy 0.650000
+  material change specular Glossy 1.000000
+  material change shininess Glossy 0.880000
+  material change mirror Glossy 0.000000
+  material change opacity Glossy 1.000000
+  material change outline Glossy 0.000000
+  material change outlinewidth Glossy 0.000000
+  material change transmode Glossy 0.000000
+  material change ambient HardPlastic 0.000000
+  material change diffuse HardPlastic 0.560000
+  material change specular HardPlastic 0.280000
+  material change shininess HardPlastic 0.690000
+  material change mirror HardPlastic 0.000000
+  material change opacity HardPlastic 1.000000
+  material change outline HardPlastic 0.000000
+  material change outlinewidth HardPlastic 0.000000
+  material change transmode HardPlastic 0.000000
+  material change ambient MetallicPastel 0.000000
+  material change diffuse MetallicPastel 0.260000
+  material change specular MetallicPastel 0.550000
+  material change shininess MetallicPastel 0.190000
+  material change mirror MetallicPastel 0.000000
+  material change opacity MetallicPastel 1.000000
+  material change outline MetallicPastel 0.000000
+  material change outlinewidth MetallicPastel 0.000000
+  material change transmode MetallicPastel 0.000000
+  material change ambient Steel 0.250000
+  material change diffuse Steel 0.000000
+  material change specular Steel 0.380000
+  material change shininess Steel 0.320000
+  material change mirror Steel 0.000000
+  material change opacity Steel 1.000000
+  material change outline Steel 0.000000
+  material change outlinewidth Steel 0.000000
+  material change transmode Steel 0.000000
+  material change ambient Translucent 0.000000
+  material change diffuse Translucent 0.700000
+  material change specular Translucent 0.600000
+  material change shininess Translucent 0.300000
+  material change mirror Translucent 0.000000
+  material change opacity Translucent 0.800000
+  material change outline Translucent 0.000000
+  material change outlinewidth Translucent 0.000000
+  material change transmode Translucent 0.000000
+  material change ambient Edgy 0.000000
+  material change diffuse Edgy 0.660000
+  material change specular Edgy 0.000000
+  material change shininess Edgy 0.750000
+  material change mirror Edgy 0.000000
+  material change opacity Edgy 1.000000
+  material change outline Edgy 0.620000
+  material change outlinewidth Edgy 0.940000
+  material change transmode Edgy 0.000000
+  material change ambient EdgyShiny 0.000000
+  material change diffuse EdgyShiny 0.660000
+  material change specular EdgyShiny 0.960000
+  material change shininess EdgyShiny 0.750000
+  material change mirror EdgyShiny 0.000000
+  material change opacity EdgyShiny 1.000000
+  material change outline EdgyShiny 0.760000
+  material change outlinewidth EdgyShiny 0.940000
+  material change transmode EdgyShiny 0.000000
+  material change ambient EdgyGlass 0.000000
+  material change diffuse EdgyGlass 0.660000
+  material change specular EdgyGlass 0.500000
+  material change shininess EdgyGlass 0.750000
+  material change mirror EdgyGlass 0.000000
+  material change opacity EdgyGlass 0.620000
+  material change outline EdgyGlass 0.620000
+  material change outlinewidth EdgyGlass 0.940000
+  material change transmode EdgyGlass 0.000000
+  material change ambient Goodsell 0.520000
+  material change diffuse Goodsell 1.000000
+  material change specular Goodsell 0.000000
+  material change shininess Goodsell -0.000000
+  material change mirror Goodsell 0.000000
+  material change opacity Goodsell 1.000000
+  material change outline Goodsell 4.000000
+  material change outlinewidth Goodsell 0.900000
+  material change transmode Goodsell 0.000000
+  material change ambient AOShiny 0.000000
+  material change diffuse AOShiny 0.850000
+  material change specular AOShiny 0.200000
+  material change shininess AOShiny 0.530000
+  material change mirror AOShiny 0.000000
+  material change opacity AOShiny 1.000000
+  material change outline AOShiny 0.000000
+  material change outlinewidth AOShiny 0.000000
+  material change transmode AOShiny 0.000000
+  material change ambient AOChalky 0.000000
+  material change diffuse AOChalky 0.850000
+  material change specular AOChalky 0.000000
+  material change shininess AOChalky 0.530000
+  material change mirror AOChalky 0.000000
+  material change opacity AOChalky 1.000000
+  material change outline AOChalky 0.000000
+  material change outlinewidth AOChalky 0.000000
+  material change transmode AOChalky 0.000000
+  material change ambient AOEdgy 0.000000
+  material change diffuse AOEdgy 0.900000
+  material change specular AOEdgy 0.200000
+  material change shininess AOEdgy 0.530000
+  material change mirror AOEdgy 0.000000
+  material change opacity AOEdgy 1.000000
+  material change outline AOEdgy 0.620000
+  material change outlinewidth AOEdgy 0.930000
+  material change transmode AOEdgy 0.000000
+  material change ambient BlownGlass 0.040000
+  material change diffuse BlownGlass 0.340000
+  material change specular BlownGlass 1.000000
+  material change shininess BlownGlass 1.000000
+  material change mirror BlownGlass 0.000000
+  material change opacity BlownGlass 0.100000
+  material change outline BlownGlass 0.000000
+  material change outlinewidth BlownGlass 0.000000
+  material change transmode BlownGlass 1.000000
+  material change ambient GlassBubble 0.250000
+  material change diffuse GlassBubble 0.340000
+  material change specular GlassBubble 1.000000
+  material change shininess GlassBubble 1.000000
+  material change mirror GlassBubble 0.000000
+  material change opacity GlassBubble 0.040000
+  material change outline GlassBubble 0.000000
+  material change outlinewidth GlassBubble 0.000000
+  material change transmode GlassBubble 1.000000
+  material change ambient RTChrome 0.000000
+  material change diffuse RTChrome 0.650000
+  material change specular RTChrome 0.500000
+  material change shininess RTChrome 0.530000
+  material change mirror RTChrome 0.700000
+  material change opacity RTChrome 1.000000
+  material change outline RTChrome 0.000000
+  material change outlinewidth RTChrome 0.000000
+  material change transmode RTChrome 0.000000
+}
+vmdrestoremymaterials
+# Atom selection macros
+atomselect macro at {resname ADE A THY T}
+atomselect macro acidic {resname ASP GLU}
+atomselect macro cyclic {resname HIS PHE PRO TRP TYR}
+atomselect macro acyclic {protein and not cyclic}
+atomselect macro aliphatic {resname ALA GLY ILE LEU VAL}
+atomselect macro alpha {protein and name CA}
+atomselect macro amino protein
+atomselect macro aromatic {resname HIS PHE TRP TYR}
+atomselect macro basic {resname ARG HIS LYS HSP}
+atomselect macro bonded {numbonds > 0}
+atomselect macro buried {resname ALA LEU VAL ILE PHE CYS MET TRP}
+atomselect macro cg {resname CYT C GUA G}
+atomselect macro charged {basic or acidic}
+atomselect macro hetero {not (protein or nucleic)}
+atomselect macro hydrophobic {resname ALA LEU VAL ILE PRO PHE MET TRP}
+atomselect macro small {resname ALA GLY SER}
+atomselect macro medium {resname VAL THR ASP ASN PRO CYS ASX PCA HYP}
+atomselect macro large {protein and not (small or medium)}
+atomselect macro neutral {resname VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HYP}
+atomselect macro polar {protein and not hydrophobic}
+atomselect macro purine {resname ADE A GUA G}
+atomselect macro pyrimidine {resname CYT C THY T URA U}
+atomselect macro surface {protein and not buried}
+atomselect macro lipid {resname DLPE DMPC DPPC GPC LPPC PALM PC PGCL POPC POPE}
+atomselect macro lipids lipid
+atomselect macro ion {resname AL BA CA CAL CD CES CLA CL CO CS CU CU1 CUA HG IN IOD K LIT MG MN3 MO3 MO4 MO5 MO6 NA NAW OC7 PB POT PT RB SOD TB TL WO4 YB ZN ZN1 ZN2}
+atomselect macro ions ion
+atomselect macro sugar {resname AGLC}
+atomselect macro solvent {not (protein or sugar or nucleic or lipid)}
+atomselect macro glycan {resname NAG BGLN FUC AFUC MAN AMAN BMA BMAN}
+atomselect macro carbon {name "C.*" and not ion}
+atomselect macro hydrogen {name "[0-9]?H.*"}
+atomselect macro nitrogen {name "N.*"}
+atomselect macro oxygen {name "O.*"}
+atomselect macro sulfur {name "S.*" and not ion}
+atomselect macro noh {not hydrogen}
+atomselect macro heme {resname HEM HEME}
+atomselect macro conformationall {altloc ""}
+atomselect macro conformationA {altloc "" or altloc "A"}
+atomselect macro conformationB {altloc "" or altloc "B"}
+atomselect macro conformationC {altloc "" or altloc "C"}
+atomselect macro conformationD {altloc "" or altloc "D"}
+atomselect macro conformationE {altloc "" or altloc "E"}
+atomselect macro conformationF {altloc "" or altloc "F"}
+atomselect macro drude {type DRUD or type LP}
+atomselect macro unparametrized beta<1
+atomselect macro addedmolefacture {occupancy 0.8}
+atomselect macro qwikmd_protein {(not name QWIKMDDELETE and protein)}
+atomselect macro qwikmd_nucleic {(not name QWIKMDDELETE and nucleic)}
+atomselect macro qwikmd_glycan {(not name QWIKMDDELETE and glycan)}
+atomselect macro qwikmd_lipid {(not name QWIKMDDELETE and lipid)}
+atomselect macro qwikmd_hetero {(not name QWIKMDDELETE and hetero and not qwikmd_protein and not qwikmd_lipid and not qwikmd_nucleic and not qwikmd_glycan and not water)}
+# Display settings
+display eyesep       0.065000
+display focallength  2.000000
+display height       6.000000
+display distance     -2.000000
+display projection   Orthographic
+display nearclip set 0.010000
+display farclip  set 14.500000
+display depthcue   on
+display cuestart   0.500000
+display cueend     10.000000
+display cuestart   0.500000
+display cueend     10.000000
+display cuedensity 0.320000
+display cuemode    Linear
+display shadows off
+display ambientocclusion off
+display aoambient 0.800000
+display aodirect 0.300000
+display dof off
+display dof_fnumber 64.000000
+display dof_focaldist 0.700000
+mol new {/Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/Martini 3 complex membranes - Tutorials/Tutorial_1/example_files/symmetric-bilayer.gro} type gro first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation Lines
+mol color Name
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol clipplane center 0 0 top {0.0 0.0 0.0}
+mol clipplane color  0 0 top {0.5 0.5 0.5 }
+mol clipplane normal 0 0 top {0.0 0.0 1.0}
+mol clipplane status 0 0 top {0}
+mol clipplane center 1 0 top {0.0 0.0 0.0}
+mol clipplane color  1 0 top {0.5 0.5 0.5 }
+mol clipplane normal 1 0 top {0.0 0.0 1.0}
+mol clipplane status 1 0 top {0}
+mol clipplane center 2 0 top {0.0 0.0 0.0}
+mol clipplane color  2 0 top {0.5 0.5 0.5 }
+mol clipplane normal 2 0 top {0.0 0.0 1.0}
+mol clipplane status 2 0 top {0}
+mol clipplane center 3 0 top {0.0 0.0 0.0}
+mol clipplane color  3 0 top {0.5 0.5 0.5 }
+mol clipplane normal 3 0 top {0.0 0.0 1.0}
+mol clipplane status 3 0 top {0}
+mol clipplane center 4 0 top {0.0 0.0 0.0}
+mol clipplane color  4 0 top {0.5 0.5 0.5 }
+mol clipplane normal 4 0 top {0.0 0.0 1.0}
+mol clipplane status 4 0 top {0}
+mol clipplane center 5 0 top {0.0 0.0 0.0}
+mol clipplane color  5 0 top {0.5 0.5 0.5 }
+mol clipplane normal 5 0 top {0.0 0.0 1.0}
+mol clipplane status 5 0 top {0}
+mol rename top symmetric-bilayer.gro
+molinfo top set drawn 0
+set viewpoints([molinfo top]) {{{1 0 0 -78.1802} {0 1 0 -50.6441} {0 0 1 -59.2096} {0 0 0 1}} {{0.999974 0.00257614 -0.00368925 0} {0.00374035 -0.0200065 0.999781 0} {0.00250227 -0.999773 -0.0200166 0} {0 0 0 1}} {{0.0207042 0 0 0} {0 0.0207042 0 0} {0 0 0.0207042 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
+lappend viewplist [molinfo top]
+# done with molecule 0
+mol new {/Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/Martini 3 complex membranes - Tutorials/worked_example/1.ref_memb/POPC-CDL0-0.9-0.1-FLAT/5_PROD/md.gro} type gro first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation VDW 1.000000 12.000000
+mol color Name
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol clipplane center 0 0 top {0.0 0.0 0.0}
+mol clipplane color  0 0 top {0.5 0.5 0.5 }
+mol clipplane normal 0 0 top {0.0 0.0 1.0}
+mol clipplane status 0 0 top {0}
+mol clipplane center 1 0 top {0.0 0.0 0.0}
+mol clipplane color  1 0 top {0.5 0.5 0.5 }
+mol clipplane normal 1 0 top {0.0 0.0 1.0}
+mol clipplane status 1 0 top {0}
+mol clipplane center 2 0 top {0.0 0.0 0.0}
+mol clipplane color  2 0 top {0.5 0.5 0.5 }
+mol clipplane normal 2 0 top {0.0 0.0 1.0}
+mol clipplane status 2 0 top {0}
+mol clipplane center 3 0 top {0.0 0.0 0.0}
+mol clipplane color  3 0 top {0.5 0.5 0.5 }
+mol clipplane normal 3 0 top {0.0 0.0 1.0}
+mol clipplane status 3 0 top {0}
+mol clipplane center 4 0 top {0.0 0.0 0.0}
+mol clipplane color  4 0 top {0.5 0.5 0.5 }
+mol clipplane normal 4 0 top {0.0 0.0 1.0}
+mol clipplane status 4 0 top {0}
+mol clipplane center 5 0 top {0.0 0.0 0.0}
+mol clipplane color  5 0 top {0.5 0.5 0.5 }
+mol clipplane normal 5 0 top {0.0 0.0 1.0}
+mol clipplane status 5 0 top {0}
+mol showrep top 0 0
+mol representation VDW 1.000000 12.000000
+mol color Name
+mol selection {resname CDL0}
+mol material Opaque
+mol addrep top
+mol selupdate 1 top 0
+mol colupdate 1 top 0
+mol scaleminmax top 1 0.000000 0.000000
+mol smoothrep top 1 0
+mol drawframes top 1 {now}
+mol clipplane center 0 1 top {0.0 0.0 0.0}
+mol clipplane color  0 1 top {0.5 0.5 0.5 }
+mol clipplane normal 0 1 top {0.0 0.0 1.0}
+mol clipplane status 0 1 top {0}
+mol clipplane center 1 1 top {0.0 0.0 0.0}
+mol clipplane color  1 1 top {0.5 0.5 0.5 }
+mol clipplane normal 1 1 top {0.0 0.0 1.0}
+mol clipplane status 1 1 top {0}
+mol clipplane center 2 1 top {0.0 0.0 0.0}
+mol clipplane color  2 1 top {0.5 0.5 0.5 }
+mol clipplane normal 2 1 top {0.0 0.0 1.0}
+mol clipplane status 2 1 top {0}
+mol clipplane center 3 1 top {0.0 0.0 0.0}
+mol clipplane color  3 1 top {0.5 0.5 0.5 }
+mol clipplane normal 3 1 top {0.0 0.0 1.0}
+mol clipplane status 3 1 top {0}
+mol clipplane center 4 1 top {0.0 0.0 0.0}
+mol clipplane color  4 1 top {0.5 0.5 0.5 }
+mol clipplane normal 4 1 top {0.0 0.0 1.0}
+mol clipplane status 4 1 top {0}
+mol clipplane center 5 1 top {0.0 0.0 0.0}
+mol clipplane color  5 1 top {0.5 0.5 0.5 }
+mol clipplane normal 5 1 top {0.0 0.0 1.0}
+mol clipplane status 5 1 top {0}
+mol rename top md.gro
+molinfo top set drawn 0
+set viewpoints([molinfo top]) {{{1 0 0 -78.1802} {0 1 0 -50.6441} {0 0 1 -59.2096} {0 0 0 1}} {{0.999974 0.00257614 -0.00368925 0} {0.00374035 -0.0200065 0.999781 0} {0.00250227 -0.999773 -0.0200166 0} {0 0 0 1}} {{0.0207042 0 0 0} {0 0.0207042 0 0} {0 0 0.0207042 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
+lappend viewplist [molinfo top]
+# done with molecule 1
+mol new {/Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/Martini 3 complex membranes - Tutorials/worked_example/2.curved_memb/POPC-CDL0-0.9-0.1-CURVED/5_PROD/md.gro} type gro first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol addfile {/Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/Martini 3 complex membranes - Tutorials/worked_example/2.curved_memb/POPC-CDL0-0.9-0.1-CURVED/5_PROD/md.xtc} type xtc first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation VDW 1.400000 12.000000
+mol color ColorID 1
+mol selection {name PO4}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol clipplane center 0 0 top {0.0 0.0 0.0}
+mol clipplane color  0 0 top {0.5 0.5 0.5 }
+mol clipplane normal 0 0 top {0.0 0.0 1.0}
+mol clipplane status 0 0 top {0}
+mol clipplane center 1 0 top {0.0 0.0 0.0}
+mol clipplane color  1 0 top {0.5 0.5 0.5 }
+mol clipplane normal 1 0 top {0.0 0.0 1.0}
+mol clipplane status 1 0 top {0}
+mol clipplane center 2 0 top {0.0 0.0 0.0}
+mol clipplane color  2 0 top {0.5 0.5 0.5 }
+mol clipplane normal 2 0 top {0.0 0.0 1.0}
+mol clipplane status 2 0 top {0}
+mol clipplane center 3 0 top {0.0 0.0 0.0}
+mol clipplane color  3 0 top {0.5 0.5 0.5 }
+mol clipplane normal 3 0 top {0.0 0.0 1.0}
+mol clipplane status 3 0 top {0}
+mol clipplane center 4 0 top {0.0 0.0 0.0}
+mol clipplane color  4 0 top {0.5 0.5 0.5 }
+mol clipplane normal 4 0 top {0.0 0.0 1.0}
+mol clipplane status 4 0 top {0}
+mol clipplane center 5 0 top {0.0 0.0 0.0}
+mol clipplane color  5 0 top {0.5 0.5 0.5 }
+mol clipplane normal 5 0 top {0.0 0.0 1.0}
+mol clipplane status 5 0 top {0}
+mol representation VDW 1.000000 12.000000
+mol color ColorID 0
+mol selection {name W}
+mol material Transparent
+mol addrep top
+mol selupdate 1 top 0
+mol colupdate 1 top 0
+mol scaleminmax top 1 0.000000 0.000000
+mol smoothrep top 1 0
+mol drawframes top 1 {now}
+mol clipplane center 0 1 top {0.0 0.0 0.0}
+mol clipplane color  0 1 top {0.5 0.5 0.5 }
+mol clipplane normal 0 1 top {0.0 0.0 1.0}
+mol clipplane status 0 1 top {0}
+mol clipplane center 1 1 top {0.0 0.0 0.0}
+mol clipplane color  1 1 top {0.5 0.5 0.5 }
+mol clipplane normal 1 1 top {0.0 0.0 1.0}
+mol clipplane status 1 1 top {0}
+mol clipplane center 2 1 top {0.0 0.0 0.0}
+mol clipplane color  2 1 top {0.5 0.5 0.5 }
+mol clipplane normal 2 1 top {0.0 0.0 1.0}
+mol clipplane status 2 1 top {0}
+mol clipplane center 3 1 top {0.0 0.0 0.0}
+mol clipplane color  3 1 top {0.5 0.5 0.5 }
+mol clipplane normal 3 1 top {0.0 0.0 1.0}
+mol clipplane status 3 1 top {0}
+mol clipplane center 4 1 top {0.0 0.0 0.0}
+mol clipplane color  4 1 top {0.5 0.5 0.5 }
+mol clipplane normal 4 1 top {0.0 0.0 1.0}
+mol clipplane status 4 1 top {0}
+mol clipplane center 5 1 top {0.0 0.0 0.0}
+mol clipplane color  5 1 top {0.5 0.5 0.5 }
+mol clipplane normal 5 1 top {0.0 0.0 1.0}
+mol clipplane status 5 1 top {0}
+mol representation VDW 1.100000 12.000000
+mol color ColorID 2
+mol selection {resname POPC}
+mol material Opaque
+mol addrep top
+mol selupdate 2 top 0
+mol colupdate 2 top 0
+mol scaleminmax top 2 0.000000 0.000000
+mol smoothrep top 2 0
+mol drawframes top 2 {now}
+mol clipplane center 0 2 top {0.0 0.0 0.0}
+mol clipplane color  0 2 top {0.5 0.5 0.5 }
+mol clipplane normal 0 2 top {0.0 0.0 1.0}
+mol clipplane status 0 2 top {0}
+mol clipplane center 1 2 top {0.0 0.0 0.0}
+mol clipplane color  1 2 top {0.5 0.5 0.5 }
+mol clipplane normal 1 2 top {0.0 0.0 1.0}
+mol clipplane status 1 2 top {0}
+mol clipplane center 2 2 top {0.0 0.0 0.0}
+mol clipplane color  2 2 top {0.5 0.5 0.5 }
+mol clipplane normal 2 2 top {0.0 0.0 1.0}
+mol clipplane status 2 2 top {0}
+mol clipplane center 3 2 top {0.0 0.0 0.0}
+mol clipplane color  3 2 top {0.5 0.5 0.5 }
+mol clipplane normal 3 2 top {0.0 0.0 1.0}
+mol clipplane status 3 2 top {0}
+mol clipplane center 4 2 top {0.0 0.0 0.0}
+mol clipplane color  4 2 top {0.5 0.5 0.5 }
+mol clipplane normal 4 2 top {0.0 0.0 1.0}
+mol clipplane status 4 2 top {0}
+mol clipplane center 5 2 top {0.0 0.0 0.0}
+mol clipplane color  5 2 top {0.5 0.5 0.5 }
+mol clipplane normal 5 2 top {0.0 0.0 1.0}
+mol clipplane status 5 2 top {0}
+mol showrep top 2 0
+mol rename top md.gro
+set viewpoints([molinfo top]) {{{1 0 0 -78.1802} {0 1 0 -50.6441} {0 0 1 -59.2096} {0 0 0 1}} {{0.999974 0.00257614 -0.00368925 0} {0.00374035 -0.0200065 0.999781 0} {0.00250227 -0.999773 -0.0200166 0} {0 0 0 1}} {{0.0207042 0 0 0} {0 0.0207042 0 0} {0 0 0.0207042 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
+lappend viewplist [molinfo top]
+set topmol [molinfo top]
+# done with molecule 2
+mol new /Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/RAS-Pilot2/initial-system-CG.gro type gro first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation Lines
+mol color Name
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol clipplane center 0 0 top {0.0 0.0 0.0}
+mol clipplane color  0 0 top {0.5 0.5 0.5 }
+mol clipplane normal 0 0 top {0.0 0.0 1.0}
+mol clipplane status 0 0 top {0}
+mol clipplane center 1 0 top {0.0 0.0 0.0}
+mol clipplane color  1 0 top {0.5 0.5 0.5 }
+mol clipplane normal 1 0 top {0.0 0.0 1.0}
+mol clipplane status 1 0 top {0}
+mol clipplane center 2 0 top {0.0 0.0 0.0}
+mol clipplane color  2 0 top {0.5 0.5 0.5 }
+mol clipplane normal 2 0 top {0.0 0.0 1.0}
+mol clipplane status 2 0 top {0}
+mol clipplane center 3 0 top {0.0 0.0 0.0}
+mol clipplane color  3 0 top {0.5 0.5 0.5 }
+mol clipplane normal 3 0 top {0.0 0.0 1.0}
+mol clipplane status 3 0 top {0}
+mol clipplane center 4 0 top {0.0 0.0 0.0}
+mol clipplane color  4 0 top {0.5 0.5 0.5 }
+mol clipplane normal 4 0 top {0.0 0.0 1.0}
+mol clipplane status 4 0 top {0}
+mol clipplane center 5 0 top {0.0 0.0 0.0}
+mol clipplane color  5 0 top {0.5 0.5 0.5 }
+mol clipplane normal 5 0 top {0.0 0.0 1.0}
+mol clipplane status 5 0 top {0}
+mol showrep top 0 0
+mol representation VDW 1.000000 12.000000
+mol color Name
+mol selection {name PO4}
+mol material Opaque
+mol addrep top
+mol selupdate 1 top 0
+mol colupdate 1 top 0
+mol scaleminmax top 1 0.000000 0.000000
+mol smoothrep top 1 0
+mol drawframes top 1 {now}
+mol clipplane center 0 1 top {0.0 0.0 0.0}
+mol clipplane color  0 1 top {0.5 0.5 0.5 }
+mol clipplane normal 0 1 top {0.0 0.0 1.0}
+mol clipplane status 0 1 top {0}
+mol clipplane center 1 1 top {0.0 0.0 0.0}
+mol clipplane color  1 1 top {0.5 0.5 0.5 }
+mol clipplane normal 1 1 top {0.0 0.0 1.0}
+mol clipplane status 1 1 top {0}
+mol clipplane center 2 1 top {0.0 0.0 0.0}
+mol clipplane color  2 1 top {0.5 0.5 0.5 }
+mol clipplane normal 2 1 top {0.0 0.0 1.0}
+mol clipplane status 2 1 top {0}
+mol clipplane center 3 1 top {0.0 0.0 0.0}
+mol clipplane color  3 1 top {0.5 0.5 0.5 }
+mol clipplane normal 3 1 top {0.0 0.0 1.0}
+mol clipplane status 3 1 top {0}
+mol clipplane center 4 1 top {0.0 0.0 0.0}
+mol clipplane color  4 1 top {0.5 0.5 0.5 }
+mol clipplane normal 4 1 top {0.0 0.0 1.0}
+mol clipplane status 4 1 top {0}
+mol clipplane center 5 1 top {0.0 0.0 0.0}
+mol clipplane color  5 1 top {0.5 0.5 0.5 }
+mol clipplane normal 5 1 top {0.0 0.0 1.0}
+mol clipplane status 5 1 top {0}
+mol representation VDW 1.000000 12.000000
+mol color Name
+mol selection {name BB}
+mol material Opaque
+mol addrep top
+mol selupdate 2 top 0
+mol colupdate 2 top 0
+mol scaleminmax top 2 0.000000 0.000000
+mol smoothrep top 2 0
+mol drawframes top 2 {now}
+mol clipplane center 0 2 top {0.0 0.0 0.0}
+mol clipplane color  0 2 top {0.5 0.5 0.5 }
+mol clipplane normal 0 2 top {0.0 0.0 1.0}
+mol clipplane status 0 2 top {0}
+mol clipplane center 1 2 top {0.0 0.0 0.0}
+mol clipplane color  1 2 top {0.5 0.5 0.5 }
+mol clipplane normal 1 2 top {0.0 0.0 1.0}
+mol clipplane status 1 2 top {0}
+mol clipplane center 2 2 top {0.0 0.0 0.0}
+mol clipplane color  2 2 top {0.5 0.5 0.5 }
+mol clipplane normal 2 2 top {0.0 0.0 1.0}
+mol clipplane status 2 2 top {0}
+mol clipplane center 3 2 top {0.0 0.0 0.0}
+mol clipplane color  3 2 top {0.5 0.5 0.5 }
+mol clipplane normal 3 2 top {0.0 0.0 1.0}
+mol clipplane status 3 2 top {0}
+mol clipplane center 4 2 top {0.0 0.0 0.0}
+mol clipplane color  4 2 top {0.5 0.5 0.5 }
+mol clipplane normal 4 2 top {0.0 0.0 1.0}
+mol clipplane status 4 2 top {0}
+mol clipplane center 5 2 top {0.0 0.0 0.0}
+mol clipplane color  5 2 top {0.5 0.5 0.5 }
+mol clipplane normal 5 2 top {0.0 0.0 1.0}
+mol clipplane status 5 2 top {0}
+mol rename top initial-system-CG.gro
+molinfo top set drawn 0
+set viewpoints([molinfo top]) {{{1 0 0 -78.1802} {0 1 0 -50.6441} {0 0 1 -59.2096} {0 0 0 1}} {{0.999974 0.00257614 -0.00368925 0} {0.00374035 -0.0200065 0.999781 0} {0.00250227 -0.999773 -0.0200166 0} {0 0 0 1}} {{0.0207042 0 0 0} {0 0.0207042 0 0} {0 0 0.0207042 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
+lappend viewplist [molinfo top]
+# done with molecule 3
+foreach v $viewplist {
+  molinfo $v set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($v)
+}
+foreach v $fixedlist {
+  molinfo $v set fixed 1
+}
+unset viewplist
+unset fixedlist
+mol top $topmol
+unset topmol
+proc vmdrestoremycolors {} {
+color scale colors RWB {1.0 0.0 0.0} {1.0 1.0 1.0} {0.0 0.0 1.0}
+color scale colors BWR {0.0 0.0 1.0} {1.0 1.0 1.0} {1.0 0.0 0.0}
+color scale colors RGryB {1.0 0.0 0.0} {0.5 0.5 0.5} {0.0 0.0 1.0}
+color scale colors BGryR {0.0 0.0 1.0} {0.5 0.5 0.5} {1.0 0.0 0.0}
+color scale colors RGB {1.0 0.0 0.0} {0.0 1.0 0.0} {0.0 0.0 1.0}
+color scale colors BGR {0.0 0.0 1.0} {0.0 1.0 0.0} {1.0 0.0 0.0}
+color scale colors RWG {1.0 0.0 0.0} {1.0 1.0 1.0} {0.0 1.0 0.0}
+color scale colors GWR {0.0 1.0 0.0} {1.0 1.0 1.0} {1.0 0.0 0.0}
+color scale colors GWB {0.0 1.0 0.0} {1.0 1.0 1.0} {0.0 0.0 1.0}
+color scale colors BWG {0.0 0.0 1.0} {1.0 1.0 1.0} {0.0 1.0 0.0}
+color scale colors BlkW {0.0 0.0 0.0} {0.5 0.5 0.5} {1.0 1.0 1.0}
+color scale colors WBlk {1.0 1.0 1.0} {0.5 0.5 0.5} {0.0 0.0 0.0}
+color scale colors cividis {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors viridis {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors magma {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors plasma {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors inferno {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L3 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L8 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L9 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L16 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L17 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L18 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L19 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L20 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_C2 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_C4 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_C6 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_C7 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_I1 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_I2 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_I3 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_D11 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_D12 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors turbo {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_R2 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+  color scale method RWB
+  set colorcmds {
+    {color Display {Background} white}
+    {color Display {BackgroundTop} black}
+    {color Display {BackgroundBot} blue2}
+    {color Display {FPS} white}
+    {color Axes {Labels} black}
+    {color Name {LPA} green}
+    {color Name {LPB} green}
+    {color Name {G} pink}
+    {color Name {D} cyan}
+    {color Name {R} purple}
+    {color Name {W} lime}
+    {color Name {A} mauve}
+    {color Name {T} ochre}
+    {color Name {B} iceblue}
+    {color Name {F} black}
+    {color Name {M} yellow2}
+    {color Type {LP} green}
+    {color Type {DRUD} pink}
+    {color Type {G} pink}
+    {color Type {D} cyan}
+    {color Type {R} purple}
+    {color Type {W} lime}
+    {color Type {A} mauve}
+    {color Type {T} ochre}
+    {color Type {B} iceblue}
+    {color Type {F} black}
+    {color Type {M} yellow2}
+    {color Element {X} cyan}
+    {color Element {Ac} ochre}
+    {color Element {Ag} ochre}
+    {color Element {Al} ochre}
+    {color Element {Am} ochre}
+    {color Element {Ar} ochre}
+    {color Element {As} ochre}
+    {color Element {At} ochre}
+    {color Element {Au} ochre}
+    {color Element {B} ochre}
+    {color Element {Ba} ochre}
+    {color Element {Be} ochre}
+    {color Element {Bh} ochre}
+    {color Element {Bi} ochre}
+    {color Element {Bk} ochre}
+    {color Element {Br} ochre}
+    {color Element {Ca} ochre}
+    {color Element {Cd} ochre}
+    {color Element {Ce} ochre}
+    {color Element {Cf} ochre}
+    {color Element {Cl} ochre}
+    {color Element {Cm} ochre}
+    {color Element {Co} ochre}
+    {color Element {Cr} ochre}
+    {color Element {Cs} ochre}
+    {color Element {Cu} ochre}
+    {color Element {Db} ochre}
+    {color Element {Ds} ochre}
+    {color Element {Dy} ochre}
+    {color Element {Er} ochre}
+    {color Element {Es} ochre}
+    {color Element {Eu} ochre}
+    {color Element {F} ochre}
+    {color Element {Fe} ochre}
+    {color Element {Fm} ochre}
+    {color Element {Fr} ochre}
+    {color Element {Ga} ochre}
+    {color Element {Gd} ochre}
+    {color Element {Ge} ochre}
+    {color Element {He} ochre}
+    {color Element {Hf} ochre}
+    {color Element {Hg} ochre}
+    {color Element {Ho} ochre}
+    {color Element {Hs} ochre}
+    {color Element {I} ochre}
+    {color Element {In} ochre}
+    {color Element {Ir} ochre}
+    {color Element {K} ochre}
+    {color Element {Kr} ochre}
+    {color Element {La} ochre}
+    {color Element {Li} ochre}
+    {color Element {Lr} ochre}
+    {color Element {Lu} ochre}
+    {color Element {Md} ochre}
+    {color Element {Mg} ochre}
+    {color Element {Mn} ochre}
+    {color Element {Mo} ochre}
+    {color Element {Mt} ochre}
+    {color Element {Na} ochre}
+    {color Element {Nb} ochre}
+    {color Element {Nd} ochre}
+    {color Element {Ne} ochre}
+    {color Element {Ni} ochre}
+    {color Element {No} ochre}
+    {color Element {Np} ochre}
+    {color Element {Os} ochre}
+    {color Element {Pa} ochre}
+    {color Element {Pb} ochre}
+    {color Element {Pd} ochre}
+    {color Element {Pm} ochre}
+    {color Element {Po} ochre}
+    {color Element {Pr} ochre}
+    {color Element {Pt} ochre}
+    {color Element {Pu} ochre}
+    {color Element {Ra} ochre}
+    {color Element {Rb} ochre}
+    {color Element {Re} ochre}
+    {color Element {Rf} ochre}
+    {color Element {Rg} ochre}
+    {color Element {Rh} ochre}
+    {color Element {Rn} ochre}
+    {color Element {Ru} ochre}
+    {color Element {Sb} ochre}
+    {color Element {Sc} ochre}
+    {color Element {Se} ochre}
+    {color Element {Sg} ochre}
+    {color Element {Si} ochre}
+    {color Element {Sm} ochre}
+    {color Element {Sn} ochre}
+    {color Element {Sr} ochre}
+    {color Element {Ta} ochre}
+    {color Element {Tb} ochre}
+    {color Element {Tc} ochre}
+    {color Element {Te} ochre}
+    {color Element {Th} ochre}
+    {color Element {Ti} ochre}
+    {color Element {Tl} ochre}
+    {color Element {Tm} ochre}
+    {color Element {U} ochre}
+    {color Element {V} ochre}
+    {color Element {W} ochre}
+    {color Element {Xe} ochre}
+    {color Element {Y} ochre}
+    {color Element {Yb} ochre}
+    {color Element {Zr} ochre}
+    {color Resname {DPPC} silver}
+    {color Resname {DOPC} green}
+    {color Resname {CHOL} white}
+    {color Resname {W} pink}
+    {color Resname {POPC} cyan}
+    {color Resname {CDL0} purple}
+    {color Resname {ION} lime}
+    {color Resname {wall} mauve}
+    {color Resname {POPX} ochre}
+    {color Resname {DIPE} iceblue}
+    {color Resname {DPSM} black}
+    {color Resname {PAPC} yellow2}
+    {color Resname {POPE} yellow3}
+    {color Resname {PAPS} green2}
+    {color Resname {PAP6} green3}
+    {color Resname {ACE1} cyan2}
+    {color Resname {CYF} cyan3}
+    {color Resname {ACE2} blue2}
+    {color Resname {CYM} blue3}
+    {color Resname {NMA} violet}
+    {color Resname {GTP} violet2}
+    {color Resname {MG} magenta}
+    {color Resname {HOH} magenta2}
+    {color Chain {X} blue}
+    {color Segname {} blue}
+    {color Conformation {all} blue}
+    {color Molecule {0} blue}
+    {color Molecule {1} red}
+    {color Molecule {2} gray}
+    {color Molecule {3} orange}
+    {color Structure {3_10_Helix} blue}
+    {color Surface {Grasp} gray}
+    {color Labels {Springs} orange}
+    {color Stage {Even} gray}
+    {color Stage {Odd} silver}
+  }
+  foreach colcmd $colorcmds {
+    set val [catch {eval $colcmd}]
+  }
+  color change rgb 0 0.0 0.0 1.0
+  color change rgb 2 0.3499999940395355 0.3499999940395355 0.3499999940395355
+  color change rgb 3 1.0 0.5 0.0
+  color change rgb 4 1.0 1.0 0.0
+  color change rgb 5 0.5 0.5 0.20000000298023224
+  color change rgb 6 0.6000000238418579 0.6000000238418579 0.6000000238418579
+  color change rgb 7 0.0 1.0 0.0
+  color change rgb 9 1.0 0.6000000238418579 0.6000000238418579
+  color change rgb 11 0.6499999761581421 0.0 0.6499999761581421
+  color change rgb 12 0.5 0.8999999761581421 0.4000000059604645
+  color change rgb 13 0.8999999761581421 0.4000000059604645 0.699999988079071
+  color change rgb 14 0.5 0.30000001192092896 0.0
+  color change rgb 15 0.5 0.5 0.75
+  color change rgb 17 0.8799999952316284 0.9700000286102295 0.019999999552965164
+  color change rgb 18 0.550000011920929 0.8999999761581421 0.019999999552965164
+  color change rgb 19 0.0 0.8999999761581421 0.03999999910593033
+  color change rgb 20 0.0 0.8999999761581421 0.5
+  color change rgb 21 0.0 0.8799999952316284 1.0
+  color change rgb 22 0.0 0.7599999904632568 1.0
+  color change rgb 23 0.019999999552965164 0.3799999952316284 0.6700000166893005
+  color change rgb 24 0.009999999776482582 0.03999999910593033 0.9300000071525574
+  color change rgb 25 0.27000001072883606 0.0 0.9800000190734863
+  color change rgb 26 0.44999998807907104 0.0 0.8999999761581421
+  color change rgb 27 0.8999999761581421 0.0 0.8999999761581421
+  color change rgb 28 1.0 0.0 0.6600000262260437
+  color change rgb 29 0.9800000190734863 0.0 0.23000000417232513
+  color change rgb 30 0.8100000023841858 0.0 0.0
+  color change rgb 31 0.8899999856948853 0.3499999940395355 0.0
+  color change rgb 32 0.9599999785423279 0.7200000286102295 0.0
+}
+vmdrestoremycolors
+label textsize 1.0

molecular_vis/workflows/curved-membrane/task_description.txt

@@ -0,0 +1,11 @@
+1. Please load the Martini coarse-grained simulation file from "curved-membrane/data/curved-membrane.".
+
+2. Use VMD to show a zoomed in view of the membrane side coloring the water blue and the lipid phosphate (PO4 beads) red, and take a screenshot.
+
+3. Analyze the visualization and answer the following questions:
+Q1: Is there any water that penetrates into the membrane phase? (yes/no)
+
+4. Save your work:
+Save the VMD state as "curved-membrane/results/{agent_mode}/curved-membrane.vmd".
+Save the screenshot of the visualization as "curved-membrane/results/{agent_mode}/curved-membrane.png".
+Save the answers to the analysis questions in plain text as "curved-membrane/results/{agent_mode}/answers.txt".

molecular_vis/workflows/curved-membrane/visualization_goals.txt

@@ -0,0 +1,7 @@
+vision:
+1. Does the visualization should show the side of the bilayer, with water above and below and mostly empty space in the middle where the bilayer core is
+
+text:
+1. Q1 correct answer: Yes
+
+# Q1 reason: A few water molecules can be seen a little into the membrane.

molecular_vis/workflows/ras-raf-membrane/GS/ras-raf-membrane_gs.vmd

@@ -0,0 +1,921 @@
+#!/usr/local/bin/vmd
+# VMD script written by save_state $Revision: 1.48 $
+# VMD version: 1.9.4a57
+set viewplist {}
+set fixedlist {}
+proc vmdrestoremymaterials {} {
+  set mlist { Opaque Transparent BrushedMetal Diffuse Ghost Glass1 Glass2 Glass3 Glossy HardPlastic MetallicPastel Steel Translucent Edgy EdgyShiny EdgyGlass Goodsell AOShiny AOChalky AOEdgy BlownGlass GlassBubble RTChrome }
+  set mymlist [material list]
+  foreach mat $mlist {
+    if { [lsearch $mymlist $mat] == -1 } { 
+      material add $mat
+    }
+  }
+  material change ambient Opaque 0.000000
+  material change diffuse Opaque 0.650000
+  material change specular Opaque 0.500000
+  material change shininess Opaque 0.534020
+  material change mirror Opaque 0.000000
+  material change opacity Opaque 1.000000
+  material change outline Opaque 0.000000
+  material change outlinewidth Opaque 0.000000
+  material change transmode Opaque 0.000000
+  material change ambient Transparent 0.000000
+  material change diffuse Transparent 0.650000
+  material change specular Transparent 0.500000
+  material change shininess Transparent 0.534020
+  material change mirror Transparent 0.000000
+  material change opacity Transparent 0.300000
+  material change outline Transparent 0.000000
+  material change outlinewidth Transparent 0.000000
+  material change transmode Transparent 0.000000
+  material change ambient BrushedMetal 0.080000
+  material change diffuse BrushedMetal 0.390000
+  material change specular BrushedMetal 0.340000
+  material change shininess BrushedMetal 0.150000
+  material change mirror BrushedMetal 0.000000
+  material change opacity BrushedMetal 1.000000
+  material change outline BrushedMetal 0.000000
+  material change outlinewidth BrushedMetal 0.000000
+  material change transmode BrushedMetal 0.000000
+  material change ambient Diffuse 0.000000
+  material change diffuse Diffuse 0.620000
+  material change specular Diffuse 0.000000
+  material change shininess Diffuse 0.530000
+  material change mirror Diffuse 0.000000
+  material change opacity Diffuse 1.000000
+  material change outline Diffuse 0.000000
+  material change outlinewidth Diffuse 0.000000
+  material change transmode Diffuse 0.000000
+  material change ambient Ghost 0.000000
+  material change diffuse Ghost 0.000000
+  material change specular Ghost 1.000000
+  material change shininess Ghost 0.230000
+  material change mirror Ghost 0.000000
+  material change opacity Ghost 0.100000
+  material change outline Ghost 0.000000
+  material change outlinewidth Ghost 0.000000
+  material change transmode Ghost 0.000000
+  material change ambient Glass1 0.000000
+  material change diffuse Glass1 0.500000
+  material change specular Glass1 0.650000
+  material change shininess Glass1 0.530000
+  material change mirror Glass1 0.000000
+  material change opacity Glass1 0.150000
+  material change outline Glass1 0.000000
+  material change outlinewidth Glass1 0.000000
+  material change transmode Glass1 0.000000
+  material change ambient Glass2 0.520000
+  material change diffuse Glass2 0.760000
+  material change specular Glass2 0.220000
+  material change shininess Glass2 0.590000
+  material change mirror Glass2 0.000000
+  material change opacity Glass2 0.680000
+  material change outline Glass2 0.000000
+  material change outlinewidth Glass2 0.000000
+  material change transmode Glass2 0.000000
+  material change ambient Glass3 0.150000
+  material change diffuse Glass3 0.250000
+  material change specular Glass3 0.750000
+  material change shininess Glass3 0.800000
+  material change mirror Glass3 0.000000
+  material change opacity Glass3 0.500000
+  material change outline Glass3 0.000000
+  material change outlinewidth Glass3 0.000000
+  material change transmode Glass3 0.000000
+  material change ambient Glossy 0.000000
+  material change diffuse Glossy 0.650000
+  material change specular Glossy 1.000000
+  material change shininess Glossy 0.880000
+  material change mirror Glossy 0.000000
+  material change opacity Glossy 1.000000
+  material change outline Glossy 0.000000
+  material change outlinewidth Glossy 0.000000
+  material change transmode Glossy 0.000000
+  material change ambient HardPlastic 0.000000
+  material change diffuse HardPlastic 0.560000
+  material change specular HardPlastic 0.280000
+  material change shininess HardPlastic 0.690000
+  material change mirror HardPlastic 0.000000
+  material change opacity HardPlastic 1.000000
+  material change outline HardPlastic 0.000000
+  material change outlinewidth HardPlastic 0.000000
+  material change transmode HardPlastic 0.000000
+  material change ambient MetallicPastel 0.000000
+  material change diffuse MetallicPastel 0.260000
+  material change specular MetallicPastel 0.550000
+  material change shininess MetallicPastel 0.190000
+  material change mirror MetallicPastel 0.000000
+  material change opacity MetallicPastel 1.000000
+  material change outline MetallicPastel 0.000000
+  material change outlinewidth MetallicPastel 0.000000
+  material change transmode MetallicPastel 0.000000
+  material change ambient Steel 0.250000
+  material change diffuse Steel 0.000000
+  material change specular Steel 0.380000
+  material change shininess Steel 0.320000
+  material change mirror Steel 0.000000
+  material change opacity Steel 1.000000
+  material change outline Steel 0.000000
+  material change outlinewidth Steel 0.000000
+  material change transmode Steel 0.000000
+  material change ambient Translucent 0.000000
+  material change diffuse Translucent 0.700000
+  material change specular Translucent 0.600000
+  material change shininess Translucent 0.300000
+  material change mirror Translucent 0.000000
+  material change opacity Translucent 0.800000
+  material change outline Translucent 0.000000
+  material change outlinewidth Translucent 0.000000
+  material change transmode Translucent 0.000000
+  material change ambient Edgy 0.000000
+  material change diffuse Edgy 0.660000
+  material change specular Edgy 0.000000
+  material change shininess Edgy 0.750000
+  material change mirror Edgy 0.000000
+  material change opacity Edgy 1.000000
+  material change outline Edgy 0.620000
+  material change outlinewidth Edgy 0.940000
+  material change transmode Edgy 0.000000
+  material change ambient EdgyShiny 0.000000
+  material change diffuse EdgyShiny 0.660000
+  material change specular EdgyShiny 0.960000
+  material change shininess EdgyShiny 0.750000
+  material change mirror EdgyShiny 0.000000
+  material change opacity EdgyShiny 1.000000
+  material change outline EdgyShiny 0.760000
+  material change outlinewidth EdgyShiny 0.940000
+  material change transmode EdgyShiny 0.000000
+  material change ambient EdgyGlass 0.000000
+  material change diffuse EdgyGlass 0.660000
+  material change specular EdgyGlass 0.500000
+  material change shininess EdgyGlass 0.750000
+  material change mirror EdgyGlass 0.000000
+  material change opacity EdgyGlass 0.620000
+  material change outline EdgyGlass 0.620000
+  material change outlinewidth EdgyGlass 0.940000
+  material change transmode EdgyGlass 0.000000
+  material change ambient Goodsell 0.520000
+  material change diffuse Goodsell 1.000000
+  material change specular Goodsell 0.000000
+  material change shininess Goodsell -0.000000
+  material change mirror Goodsell 0.000000
+  material change opacity Goodsell 1.000000
+  material change outline Goodsell 4.000000
+  material change outlinewidth Goodsell 0.900000
+  material change transmode Goodsell 0.000000
+  material change ambient AOShiny 0.000000
+  material change diffuse AOShiny 0.850000
+  material change specular AOShiny 0.200000
+  material change shininess AOShiny 0.530000
+  material change mirror AOShiny 0.000000
+  material change opacity AOShiny 1.000000
+  material change outline AOShiny 0.000000
+  material change outlinewidth AOShiny 0.000000
+  material change transmode AOShiny 0.000000
+  material change ambient AOChalky 0.000000
+  material change diffuse AOChalky 0.850000
+  material change specular AOChalky 0.000000
+  material change shininess AOChalky 0.530000
+  material change mirror AOChalky 0.000000
+  material change opacity AOChalky 1.000000
+  material change outline AOChalky 0.000000
+  material change outlinewidth AOChalky 0.000000
+  material change transmode AOChalky 0.000000
+  material change ambient AOEdgy 0.000000
+  material change diffuse AOEdgy 0.900000
+  material change specular AOEdgy 0.200000
+  material change shininess AOEdgy 0.530000
+  material change mirror AOEdgy 0.000000
+  material change opacity AOEdgy 1.000000
+  material change outline AOEdgy 0.620000
+  material change outlinewidth AOEdgy 0.930000
+  material change transmode AOEdgy 0.000000
+  material change ambient BlownGlass 0.040000
+  material change diffuse BlownGlass 0.340000
+  material change specular BlownGlass 1.000000
+  material change shininess BlownGlass 1.000000
+  material change mirror BlownGlass 0.000000
+  material change opacity BlownGlass 0.100000
+  material change outline BlownGlass 0.000000
+  material change outlinewidth BlownGlass 0.000000
+  material change transmode BlownGlass 1.000000
+  material change ambient GlassBubble 0.250000
+  material change diffuse GlassBubble 0.340000
+  material change specular GlassBubble 1.000000
+  material change shininess GlassBubble 1.000000
+  material change mirror GlassBubble 0.000000
+  material change opacity GlassBubble 0.040000
+  material change outline GlassBubble 0.000000
+  material change outlinewidth GlassBubble 0.000000
+  material change transmode GlassBubble 1.000000
+  material change ambient RTChrome 0.000000
+  material change diffuse RTChrome 0.650000
+  material change specular RTChrome 0.500000
+  material change shininess RTChrome 0.530000
+  material change mirror RTChrome 0.700000
+  material change opacity RTChrome 1.000000
+  material change outline RTChrome 0.000000
+  material change outlinewidth RTChrome 0.000000
+  material change transmode RTChrome 0.000000
+}
+vmdrestoremymaterials
+# Atom selection macros
+atomselect macro at {resname ADE A THY T}
+atomselect macro acidic {resname ASP GLU}
+atomselect macro cyclic {resname HIS PHE PRO TRP TYR}
+atomselect macro acyclic {protein and not cyclic}
+atomselect macro aliphatic {resname ALA GLY ILE LEU VAL}
+atomselect macro alpha {protein and name CA}
+atomselect macro amino protein
+atomselect macro aromatic {resname HIS PHE TRP TYR}
+atomselect macro basic {resname ARG HIS LYS HSP}
+atomselect macro bonded {numbonds > 0}
+atomselect macro buried {resname ALA LEU VAL ILE PHE CYS MET TRP}
+atomselect macro cg {resname CYT C GUA G}
+atomselect macro charged {basic or acidic}
+atomselect macro hetero {not (protein or nucleic)}
+atomselect macro hydrophobic {resname ALA LEU VAL ILE PRO PHE MET TRP}
+atomselect macro small {resname ALA GLY SER}
+atomselect macro medium {resname VAL THR ASP ASN PRO CYS ASX PCA HYP}
+atomselect macro large {protein and not (small or medium)}
+atomselect macro neutral {resname VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HYP}
+atomselect macro polar {protein and not hydrophobic}
+atomselect macro purine {resname ADE A GUA G}
+atomselect macro pyrimidine {resname CYT C THY T URA U}
+atomselect macro surface {protein and not buried}
+atomselect macro lipid {resname DLPE DMPC DPPC GPC LPPC PALM PC PGCL POPC POPE}
+atomselect macro lipids lipid
+atomselect macro ion {resname AL BA CA CAL CD CES CLA CL CO CS CU CU1 CUA HG IN IOD K LIT MG MN3 MO3 MO4 MO5 MO6 NA NAW OC7 PB POT PT RB SOD TB TL WO4 YB ZN ZN1 ZN2}
+atomselect macro ions ion
+atomselect macro sugar {resname AGLC}
+atomselect macro solvent {not (protein or sugar or nucleic or lipid)}
+atomselect macro glycan {resname NAG BGLN FUC AFUC MAN AMAN BMA BMAN}
+atomselect macro carbon {name "C.*" and not ion}
+atomselect macro hydrogen {name "[0-9]?H.*"}
+atomselect macro nitrogen {name "N.*"}
+atomselect macro oxygen {name "O.*"}
+atomselect macro sulfur {name "S.*" and not ion}
+atomselect macro noh {not hydrogen}
+atomselect macro heme {resname HEM HEME}
+atomselect macro conformationall {altloc ""}
+atomselect macro conformationA {altloc "" or altloc "A"}
+atomselect macro conformationB {altloc "" or altloc "B"}
+atomselect macro conformationC {altloc "" or altloc "C"}
+atomselect macro conformationD {altloc "" or altloc "D"}
+atomselect macro conformationE {altloc "" or altloc "E"}
+atomselect macro conformationF {altloc "" or altloc "F"}
+atomselect macro drude {type DRUD or type LP}
+atomselect macro unparametrized beta<1
+atomselect macro addedmolefacture {occupancy 0.8}
+atomselect macro qwikmd_protein {(not name QWIKMDDELETE and protein)}
+atomselect macro qwikmd_nucleic {(not name QWIKMDDELETE and nucleic)}
+atomselect macro qwikmd_glycan {(not name QWIKMDDELETE and glycan)}
+atomselect macro qwikmd_lipid {(not name QWIKMDDELETE and lipid)}
+atomselect macro qwikmd_hetero {(not name QWIKMDDELETE and hetero and not qwikmd_protein and not qwikmd_lipid and not qwikmd_nucleic and not qwikmd_glycan and not water)}
+# Display settings
+display eyesep       0.065000
+display focallength  2.000000
+display height       6.000000
+display distance     -2.000000
+display projection   Orthographic
+display nearclip set 0.010000
+display farclip  set 14.500000
+display depthcue   on
+display cuestart   0.500000
+display cueend     10.000000
+display cuestart   0.500000
+display cueend     10.000000
+display cuedensity 0.320000
+display cuemode    Linear
+display shadows off
+display ambientocclusion off
+display aoambient 0.800000
+display aodirect 0.300000
+display dof off
+display dof_fnumber 64.000000
+display dof_focaldist 0.700000
+mol new {/Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/Martini 3 complex membranes - Tutorials/Tutorial_1/example_files/symmetric-bilayer.gro} type gro first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation Lines
+mol color Name
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol clipplane center 0 0 top {0.0 0.0 0.0}
+mol clipplane color  0 0 top {0.5 0.5 0.5 }
+mol clipplane normal 0 0 top {0.0 0.0 1.0}
+mol clipplane status 0 0 top {0}
+mol clipplane center 1 0 top {0.0 0.0 0.0}
+mol clipplane color  1 0 top {0.5 0.5 0.5 }
+mol clipplane normal 1 0 top {0.0 0.0 1.0}
+mol clipplane status 1 0 top {0}
+mol clipplane center 2 0 top {0.0 0.0 0.0}
+mol clipplane color  2 0 top {0.5 0.5 0.5 }
+mol clipplane normal 2 0 top {0.0 0.0 1.0}
+mol clipplane status 2 0 top {0}
+mol clipplane center 3 0 top {0.0 0.0 0.0}
+mol clipplane color  3 0 top {0.5 0.5 0.5 }
+mol clipplane normal 3 0 top {0.0 0.0 1.0}
+mol clipplane status 3 0 top {0}
+mol clipplane center 4 0 top {0.0 0.0 0.0}
+mol clipplane color  4 0 top {0.5 0.5 0.5 }
+mol clipplane normal 4 0 top {0.0 0.0 1.0}
+mol clipplane status 4 0 top {0}
+mol clipplane center 5 0 top {0.0 0.0 0.0}
+mol clipplane color  5 0 top {0.5 0.5 0.5 }
+mol clipplane normal 5 0 top {0.0 0.0 1.0}
+mol clipplane status 5 0 top {0}
+mol rename top symmetric-bilayer.gro
+molinfo top set drawn 0
+set viewpoints([molinfo top]) {{{1 0 0 -144.077} {0 1 0 -147.799} {0 0 1 -116.473} {0 0 0 1}} {{0.894945 0.446113 0.00229486 0} {0.00213733 -0.00943216 0.999937 0} {0.446114 -0.894889 -0.00939316 0} {0 0 0 1}} {{0.0222925 0 0 0} {0 0.0222925 0 0} {0 0 0.0222925 0} {0 0 0 1}} {{1 0 0 0.1} {0 1 0 0.52} {0 0 1 0} {0 0 0 1}}}
+lappend viewplist [molinfo top]
+# done with molecule 0
+mol new {/Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/Martini 3 complex membranes - Tutorials/worked_example/1.ref_memb/POPC-CDL0-0.9-0.1-FLAT/5_PROD/md.gro} type gro first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation VDW 1.000000 12.000000
+mol color Name
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol clipplane center 0 0 top {0.0 0.0 0.0}
+mol clipplane color  0 0 top {0.5 0.5 0.5 }
+mol clipplane normal 0 0 top {0.0 0.0 1.0}
+mol clipplane status 0 0 top {0}
+mol clipplane center 1 0 top {0.0 0.0 0.0}
+mol clipplane color  1 0 top {0.5 0.5 0.5 }
+mol clipplane normal 1 0 top {0.0 0.0 1.0}
+mol clipplane status 1 0 top {0}
+mol clipplane center 2 0 top {0.0 0.0 0.0}
+mol clipplane color  2 0 top {0.5 0.5 0.5 }
+mol clipplane normal 2 0 top {0.0 0.0 1.0}
+mol clipplane status 2 0 top {0}
+mol clipplane center 3 0 top {0.0 0.0 0.0}
+mol clipplane color  3 0 top {0.5 0.5 0.5 }
+mol clipplane normal 3 0 top {0.0 0.0 1.0}
+mol clipplane status 3 0 top {0}
+mol clipplane center 4 0 top {0.0 0.0 0.0}
+mol clipplane color  4 0 top {0.5 0.5 0.5 }
+mol clipplane normal 4 0 top {0.0 0.0 1.0}
+mol clipplane status 4 0 top {0}
+mol clipplane center 5 0 top {0.0 0.0 0.0}
+mol clipplane color  5 0 top {0.5 0.5 0.5 }
+mol clipplane normal 5 0 top {0.0 0.0 1.0}
+mol clipplane status 5 0 top {0}
+mol showrep top 0 0
+mol representation VDW 1.000000 12.000000
+mol color Name
+mol selection {resname CDL0}
+mol material Opaque
+mol addrep top
+mol selupdate 1 top 0
+mol colupdate 1 top 0
+mol scaleminmax top 1 0.000000 0.000000
+mol smoothrep top 1 0
+mol drawframes top 1 {now}
+mol clipplane center 0 1 top {0.0 0.0 0.0}
+mol clipplane color  0 1 top {0.5 0.5 0.5 }
+mol clipplane normal 0 1 top {0.0 0.0 1.0}
+mol clipplane status 0 1 top {0}
+mol clipplane center 1 1 top {0.0 0.0 0.0}
+mol clipplane color  1 1 top {0.5 0.5 0.5 }
+mol clipplane normal 1 1 top {0.0 0.0 1.0}
+mol clipplane status 1 1 top {0}
+mol clipplane center 2 1 top {0.0 0.0 0.0}
+mol clipplane color  2 1 top {0.5 0.5 0.5 }
+mol clipplane normal 2 1 top {0.0 0.0 1.0}
+mol clipplane status 2 1 top {0}
+mol clipplane center 3 1 top {0.0 0.0 0.0}
+mol clipplane color  3 1 top {0.5 0.5 0.5 }
+mol clipplane normal 3 1 top {0.0 0.0 1.0}
+mol clipplane status 3 1 top {0}
+mol clipplane center 4 1 top {0.0 0.0 0.0}
+mol clipplane color  4 1 top {0.5 0.5 0.5 }
+mol clipplane normal 4 1 top {0.0 0.0 1.0}
+mol clipplane status 4 1 top {0}
+mol clipplane center 5 1 top {0.0 0.0 0.0}
+mol clipplane color  5 1 top {0.5 0.5 0.5 }
+mol clipplane normal 5 1 top {0.0 0.0 1.0}
+mol clipplane status 5 1 top {0}
+mol rename top md.gro
+molinfo top set drawn 0
+set viewpoints([molinfo top]) {{{1 0 0 -144.077} {0 1 0 -147.799} {0 0 1 -116.473} {0 0 0 1}} {{0.894945 0.446113 0.00229486 0} {0.00213733 -0.00943216 0.999937 0} {0.446114 -0.894889 -0.00939316 0} {0 0 0 1}} {{0.0222925 0 0 0} {0 0.0222925 0 0} {0 0 0.0222925 0} {0 0 0 1}} {{1 0 0 0.1} {0 1 0 0.52} {0 0 1 0} {0 0 0 1}}}
+lappend viewplist [molinfo top]
+# done with molecule 1
+mol new {/Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/Martini 3 complex membranes - Tutorials/worked_example/2.curved_memb/POPC-CDL0-0.9-0.1-CURVED/5_PROD/md.gro} type gro first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol addfile {/Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/Martini 3 complex membranes - Tutorials/worked_example/2.curved_memb/POPC-CDL0-0.9-0.1-CURVED/5_PROD/md.xtc} type xtc first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation VDW 1.400000 12.000000
+mol color ColorID 1
+mol selection {name PO4 ROH}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol clipplane center 0 0 top {0.0 0.0 0.0}
+mol clipplane color  0 0 top {0.5 0.5 0.5 }
+mol clipplane normal 0 0 top {0.0 0.0 1.0}
+mol clipplane status 0 0 top {0}
+mol clipplane center 1 0 top {0.0 0.0 0.0}
+mol clipplane color  1 0 top {0.5 0.5 0.5 }
+mol clipplane normal 1 0 top {0.0 0.0 1.0}
+mol clipplane status 1 0 top {0}
+mol clipplane center 2 0 top {0.0 0.0 0.0}
+mol clipplane color  2 0 top {0.5 0.5 0.5 }
+mol clipplane normal 2 0 top {0.0 0.0 1.0}
+mol clipplane status 2 0 top {0}
+mol clipplane center 3 0 top {0.0 0.0 0.0}
+mol clipplane color  3 0 top {0.5 0.5 0.5 }
+mol clipplane normal 3 0 top {0.0 0.0 1.0}
+mol clipplane status 3 0 top {0}
+mol clipplane center 4 0 top {0.0 0.0 0.0}
+mol clipplane color  4 0 top {0.5 0.5 0.5 }
+mol clipplane normal 4 0 top {0.0 0.0 1.0}
+mol clipplane status 4 0 top {0}
+mol clipplane center 5 0 top {0.0 0.0 0.0}
+mol clipplane color  5 0 top {0.5 0.5 0.5 }
+mol clipplane normal 5 0 top {0.0 0.0 1.0}
+mol clipplane status 5 0 top {0}
+mol representation VDW 1.000000 12.000000
+mol color ColorID 0
+mol selection {name W}
+mol material Transparent
+mol addrep top
+mol selupdate 1 top 0
+mol colupdate 1 top 0
+mol scaleminmax top 1 0.000000 0.000000
+mol smoothrep top 1 0
+mol drawframes top 1 {now}
+mol clipplane center 0 1 top {0.0 0.0 0.0}
+mol clipplane color  0 1 top {0.5 0.5 0.5 }
+mol clipplane normal 0 1 top {0.0 0.0 1.0}
+mol clipplane status 0 1 top {0}
+mol clipplane center 1 1 top {0.0 0.0 0.0}
+mol clipplane color  1 1 top {0.5 0.5 0.5 }
+mol clipplane normal 1 1 top {0.0 0.0 1.0}
+mol clipplane status 1 1 top {0}
+mol clipplane center 2 1 top {0.0 0.0 0.0}
+mol clipplane color  2 1 top {0.5 0.5 0.5 }
+mol clipplane normal 2 1 top {0.0 0.0 1.0}
+mol clipplane status 2 1 top {0}
+mol clipplane center 3 1 top {0.0 0.0 0.0}
+mol clipplane color  3 1 top {0.5 0.5 0.5 }
+mol clipplane normal 3 1 top {0.0 0.0 1.0}
+mol clipplane status 3 1 top {0}
+mol clipplane center 4 1 top {0.0 0.0 0.0}
+mol clipplane color  4 1 top {0.5 0.5 0.5 }
+mol clipplane normal 4 1 top {0.0 0.0 1.0}
+mol clipplane status 4 1 top {0}
+mol clipplane center 5 1 top {0.0 0.0 0.0}
+mol clipplane color  5 1 top {0.5 0.5 0.5 }
+mol clipplane normal 5 1 top {0.0 0.0 1.0}
+mol clipplane status 5 1 top {0}
+mol representation VDW 1.100000 12.000000
+mol color ColorID 2
+mol selection {resname POPC}
+mol material Opaque
+mol addrep top
+mol selupdate 2 top 0
+mol colupdate 2 top 0
+mol scaleminmax top 2 0.000000 0.000000
+mol smoothrep top 2 0
+mol drawframes top 2 {now}
+mol clipplane center 0 2 top {0.0 0.0 0.0}
+mol clipplane color  0 2 top {0.5 0.5 0.5 }
+mol clipplane normal 0 2 top {0.0 0.0 1.0}
+mol clipplane status 0 2 top {0}
+mol clipplane center 1 2 top {0.0 0.0 0.0}
+mol clipplane color  1 2 top {0.5 0.5 0.5 }
+mol clipplane normal 1 2 top {0.0 0.0 1.0}
+mol clipplane status 1 2 top {0}
+mol clipplane center 2 2 top {0.0 0.0 0.0}
+mol clipplane color  2 2 top {0.5 0.5 0.5 }
+mol clipplane normal 2 2 top {0.0 0.0 1.0}
+mol clipplane status 2 2 top {0}
+mol clipplane center 3 2 top {0.0 0.0 0.0}
+mol clipplane color  3 2 top {0.5 0.5 0.5 }
+mol clipplane normal 3 2 top {0.0 0.0 1.0}
+mol clipplane status 3 2 top {0}
+mol clipplane center 4 2 top {0.0 0.0 0.0}
+mol clipplane color  4 2 top {0.5 0.5 0.5 }
+mol clipplane normal 4 2 top {0.0 0.0 1.0}
+mol clipplane status 4 2 top {0}
+mol clipplane center 5 2 top {0.0 0.0 0.0}
+mol clipplane color  5 2 top {0.5 0.5 0.5 }
+mol clipplane normal 5 2 top {0.0 0.0 1.0}
+mol clipplane status 5 2 top {0}
+mol showrep top 2 0
+mol rename top md.gro
+molinfo top set drawn 0
+set viewpoints([molinfo top]) {{{1 0 0 -144.077} {0 1 0 -147.799} {0 0 1 -116.473} {0 0 0 1}} {{0.894945 0.446113 0.00229486 0} {0.00213733 -0.00943216 0.999937 0} {0.446114 -0.894889 -0.00939316 0} {0 0 0 1}} {{0.0222925 0 0 0} {0 0.0222925 0 0} {0 0 0.0222925 0} {0 0 0 1}} {{1 0 0 0.1} {0 1 0 0.52} {0 0 1 0} {0 0 0 1}}}
+lappend viewplist [molinfo top]
+# done with molecule 2
+mol new /Users/ingolfsson1/Documents/Projects/Anthropic/SciVisAgentBench/RAS-Pilot2/initial-system-CG.gro type gro first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation Lines
+mol color Name
+mol selection {all}
+mol material Opaque
+mol addrep top
+mol selupdate 0 top 0
+mol colupdate 0 top 0
+mol scaleminmax top 0 0.000000 0.000000
+mol smoothrep top 0 0
+mol drawframes top 0 {now}
+mol clipplane center 0 0 top {0.0 0.0 0.0}
+mol clipplane color  0 0 top {0.5 0.5 0.5 }
+mol clipplane normal 0 0 top {0.0 0.0 1.0}
+mol clipplane status 0 0 top {0}
+mol clipplane center 1 0 top {0.0 0.0 0.0}
+mol clipplane color  1 0 top {0.5 0.5 0.5 }
+mol clipplane normal 1 0 top {0.0 0.0 1.0}
+mol clipplane status 1 0 top {0}
+mol clipplane center 2 0 top {0.0 0.0 0.0}
+mol clipplane color  2 0 top {0.5 0.5 0.5 }
+mol clipplane normal 2 0 top {0.0 0.0 1.0}
+mol clipplane status 2 0 top {0}
+mol clipplane center 3 0 top {0.0 0.0 0.0}
+mol clipplane color  3 0 top {0.5 0.5 0.5 }
+mol clipplane normal 3 0 top {0.0 0.0 1.0}
+mol clipplane status 3 0 top {0}
+mol clipplane center 4 0 top {0.0 0.0 0.0}
+mol clipplane color  4 0 top {0.5 0.5 0.5 }
+mol clipplane normal 4 0 top {0.0 0.0 1.0}
+mol clipplane status 4 0 top {0}
+mol clipplane center 5 0 top {0.0 0.0 0.0}
+mol clipplane color  5 0 top {0.5 0.5 0.5 }
+mol clipplane normal 5 0 top {0.0 0.0 1.0}
+mol clipplane status 5 0 top {0}
+mol showrep top 0 0
+mol representation VDW 1.000000 12.000000
+mol color ColorID 2
+mol selection {name PO4 ROH}
+mol material Opaque
+mol addrep top
+mol selupdate 1 top 0
+mol colupdate 1 top 0
+mol scaleminmax top 1 0.000000 0.000000
+mol smoothrep top 1 0
+mol drawframes top 1 {now}
+mol clipplane center 0 1 top {0.0 0.0 0.0}
+mol clipplane color  0 1 top {0.5 0.5 0.5 }
+mol clipplane normal 0 1 top {0.0 0.0 1.0}
+mol clipplane status 0 1 top {0}
+mol clipplane center 1 1 top {0.0 0.0 0.0}
+mol clipplane color  1 1 top {0.5 0.5 0.5 }
+mol clipplane normal 1 1 top {0.0 0.0 1.0}
+mol clipplane status 1 1 top {0}
+mol clipplane center 2 1 top {0.0 0.0 0.0}
+mol clipplane color  2 1 top {0.5 0.5 0.5 }
+mol clipplane normal 2 1 top {0.0 0.0 1.0}
+mol clipplane status 2 1 top {0}
+mol clipplane center 3 1 top {0.0 0.0 0.0}
+mol clipplane color  3 1 top {0.5 0.5 0.5 }
+mol clipplane normal 3 1 top {0.0 0.0 1.0}
+mol clipplane status 3 1 top {0}
+mol clipplane center 4 1 top {0.0 0.0 0.0}
+mol clipplane color  4 1 top {0.5 0.5 0.5 }
+mol clipplane normal 4 1 top {0.0 0.0 1.0}
+mol clipplane status 4 1 top {0}
+mol clipplane center 5 1 top {0.0 0.0 0.0}
+mol clipplane color  5 1 top {0.5 0.5 0.5 }
+mol clipplane normal 5 1 top {0.0 0.0 1.0}
+mol clipplane status 5 1 top {0}
+mol representation VDW 1.000000 12.000000
+mol color ColorID 1
+mol selection {name BB and resid 2 to 187}
+mol material Opaque
+mol addrep top
+mol selupdate 2 top 0
+mol colupdate 2 top 0
+mol scaleminmax top 2 0.000000 0.000000
+mol smoothrep top 2 0
+mol drawframes top 2 {now}
+mol clipplane center 0 2 top {0.0 0.0 0.0}
+mol clipplane color  0 2 top {0.5 0.5 0.5 }
+mol clipplane normal 0 2 top {0.0 0.0 1.0}
+mol clipplane status 0 2 top {0}
+mol clipplane center 1 2 top {0.0 0.0 0.0}
+mol clipplane color  1 2 top {0.5 0.5 0.5 }
+mol clipplane normal 1 2 top {0.0 0.0 1.0}
+mol clipplane status 1 2 top {0}
+mol clipplane center 2 2 top {0.0 0.0 0.0}
+mol clipplane color  2 2 top {0.5 0.5 0.5 }
+mol clipplane normal 2 2 top {0.0 0.0 1.0}
+mol clipplane status 2 2 top {0}
+mol clipplane center 3 2 top {0.0 0.0 0.0}
+mol clipplane color  3 2 top {0.5 0.5 0.5 }
+mol clipplane normal 3 2 top {0.0 0.0 1.0}
+mol clipplane status 3 2 top {0}
+mol clipplane center 4 2 top {0.0 0.0 0.0}
+mol clipplane color  4 2 top {0.5 0.5 0.5 }
+mol clipplane normal 4 2 top {0.0 0.0 1.0}
+mol clipplane status 4 2 top {0}
+mol clipplane center 5 2 top {0.0 0.0 0.0}
+mol clipplane color  5 2 top {0.5 0.5 0.5 }
+mol clipplane normal 5 2 top {0.0 0.0 1.0}
+mol clipplane status 5 2 top {0}
+mol representation VDW 1.000000 12.000000
+mol color ColorID 0
+mol selection {name BB and resid 188 to 329}
+mol material Opaque
+mol addrep top
+mol selupdate 3 top 0
+mol colupdate 3 top 0
+mol scaleminmax top 3 0.000000 0.000000
+mol smoothrep top 3 0
+mol drawframes top 3 {now}
+mol clipplane center 0 3 top {0.0 0.0 0.0}
+mol clipplane color  0 3 top {0.5 0.5 0.5 }
+mol clipplane normal 0 3 top {0.0 0.0 1.0}
+mol clipplane status 0 3 top {0}
+mol clipplane center 1 3 top {0.0 0.0 0.0}
+mol clipplane color  1 3 top {0.5 0.5 0.5 }
+mol clipplane normal 1 3 top {0.0 0.0 1.0}
+mol clipplane status 1 3 top {0}
+mol clipplane center 2 3 top {0.0 0.0 0.0}
+mol clipplane color  2 3 top {0.5 0.5 0.5 }
+mol clipplane normal 2 3 top {0.0 0.0 1.0}
+mol clipplane status 2 3 top {0}
+mol clipplane center 3 3 top {0.0 0.0 0.0}
+mol clipplane color  3 3 top {0.5 0.5 0.5 }
+mol clipplane normal 3 3 top {0.0 0.0 1.0}
+mol clipplane status 3 3 top {0}
+mol clipplane center 4 3 top {0.0 0.0 0.0}
+mol clipplane color  4 3 top {0.5 0.5 0.5 }
+mol clipplane normal 4 3 top {0.0 0.0 1.0}
+mol clipplane status 4 3 top {0}
+mol clipplane center 5 3 top {0.0 0.0 0.0}
+mol clipplane color  5 3 top {0.5 0.5 0.5 }
+mol clipplane normal 5 3 top {0.0 0.0 1.0}
+mol clipplane status 5 3 top {0}
+mol rename top initial-system-CG.gro
+set viewpoints([molinfo top]) {{{1 0 0 -144.077} {0 1 0 -147.799} {0 0 1 -116.473} {0 0 0 1}} {{0.894945 0.446113 0.00229486 0} {0.00213733 -0.00943216 0.999937 0} {0.446114 -0.894889 -0.00939316 0} {0 0 0 1}} {{0.0222925 0 0 0} {0 0.0222925 0 0} {0 0 0.0222925 0} {0 0 0 1}} {{1 0 0 0.1} {0 1 0 0.52} {0 0 1 0} {0 0 0 1}}}
+lappend viewplist [molinfo top]
+set topmol [molinfo top]
+# done with molecule 3
+foreach v $viewplist {
+  molinfo $v set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($v)
+}
+foreach v $fixedlist {
+  molinfo $v set fixed 1
+}
+unset viewplist
+unset fixedlist
+mol top $topmol
+unset topmol
+proc vmdrestoremycolors {} {
+color scale colors RWB {1.0 0.0 0.0} {1.0 1.0 1.0} {0.0 0.0 1.0}
+color scale colors BWR {0.0 0.0 1.0} {1.0 1.0 1.0} {1.0 0.0 0.0}
+color scale colors RGryB {1.0 0.0 0.0} {0.5 0.5 0.5} {0.0 0.0 1.0}
+color scale colors BGryR {0.0 0.0 1.0} {0.5 0.5 0.5} {1.0 0.0 0.0}
+color scale colors RGB {1.0 0.0 0.0} {0.0 1.0 0.0} {0.0 0.0 1.0}
+color scale colors BGR {0.0 0.0 1.0} {0.0 1.0 0.0} {1.0 0.0 0.0}
+color scale colors RWG {1.0 0.0 0.0} {1.0 1.0 1.0} {0.0 1.0 0.0}
+color scale colors GWR {0.0 1.0 0.0} {1.0 1.0 1.0} {1.0 0.0 0.0}
+color scale colors GWB {0.0 1.0 0.0} {1.0 1.0 1.0} {0.0 0.0 1.0}
+color scale colors BWG {0.0 0.0 1.0} {1.0 1.0 1.0} {0.0 1.0 0.0}
+color scale colors BlkW {0.0 0.0 0.0} {0.5 0.5 0.5} {1.0 1.0 1.0}
+color scale colors WBlk {1.0 1.0 1.0} {0.5 0.5 0.5} {0.0 0.0 0.0}
+color scale colors cividis {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors viridis {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors magma {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors plasma {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors inferno {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L3 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L8 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L9 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L16 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L17 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L18 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L19 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_L20 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_C2 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_C4 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_C6 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_C7 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_I1 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_I2 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_I3 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_D11 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_D12 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors turbo {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+color scale colors CET_R2 {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}
+  color scale method RWB
+  set colorcmds {
+    {color Display {Background} white}
+    {color Display {BackgroundTop} black}
+    {color Display {BackgroundBot} blue2}
+    {color Display {FPS} white}
+    {color Axes {Labels} black}
+    {color Name {LPA} green}
+    {color Name {LPB} green}
+    {color Name {G} pink}
+    {color Name {D} cyan}
+    {color Name {R} purple}
+    {color Name {W} lime}
+    {color Name {A} mauve}
+    {color Name {T} ochre}
+    {color Name {B} iceblue}
+    {color Name {F} black}
+    {color Name {M} yellow2}
+    {color Type {LP} green}
+    {color Type {DRUD} pink}
+    {color Type {G} pink}
+    {color Type {D} cyan}
+    {color Type {R} purple}
+    {color Type {W} lime}
+    {color Type {A} mauve}
+    {color Type {T} ochre}
+    {color Type {B} iceblue}
+    {color Type {F} black}
+    {color Type {M} yellow2}
+    {color Element {X} cyan}
+    {color Element {Ac} ochre}
+    {color Element {Ag} ochre}
+    {color Element {Al} ochre}
+    {color Element {Am} ochre}
+    {color Element {Ar} ochre}
+    {color Element {As} ochre}
+    {color Element {At} ochre}
+    {color Element {Au} ochre}
+    {color Element {B} ochre}
+    {color Element {Ba} ochre}
+    {color Element {Be} ochre}
+    {color Element {Bh} ochre}
+    {color Element {Bi} ochre}
+    {color Element {Bk} ochre}
+    {color Element {Br} ochre}
+    {color Element {Ca} ochre}
+    {color Element {Cd} ochre}
+    {color Element {Ce} ochre}
+    {color Element {Cf} ochre}
+    {color Element {Cl} ochre}
+    {color Element {Cm} ochre}
+    {color Element {Co} ochre}
+    {color Element {Cr} ochre}
+    {color Element {Cs} ochre}
+    {color Element {Cu} ochre}
+    {color Element {Db} ochre}
+    {color Element {Ds} ochre}
+    {color Element {Dy} ochre}
+    {color Element {Er} ochre}
+    {color Element {Es} ochre}
+    {color Element {Eu} ochre}
+    {color Element {F} ochre}
+    {color Element {Fe} ochre}
+    {color Element {Fm} ochre}
+    {color Element {Fr} ochre}
+    {color Element {Ga} ochre}
+    {color Element {Gd} ochre}
+    {color Element {Ge} ochre}
+    {color Element {He} ochre}
+    {color Element {Hf} ochre}
+    {color Element {Hg} ochre}
+    {color Element {Ho} ochre}
+    {color Element {Hs} ochre}
+    {color Element {I} ochre}
+    {color Element {In} ochre}
+    {color Element {Ir} ochre}
+    {color Element {K} ochre}
+    {color Element {Kr} ochre}
+    {color Element {La} ochre}
+    {color Element {Li} ochre}
+    {color Element {Lr} ochre}
+    {color Element {Lu} ochre}
+    {color Element {Md} ochre}
+    {color Element {Mg} ochre}
+    {color Element {Mn} ochre}
+    {color Element {Mo} ochre}
+    {color Element {Mt} ochre}
+    {color Element {Na} ochre}
+    {color Element {Nb} ochre}
+    {color Element {Nd} ochre}
+    {color Element {Ne} ochre}
+    {color Element {Ni} ochre}
+    {color Element {No} ochre}
+    {color Element {Np} ochre}
+    {color Element {Os} ochre}
+    {color Element {Pa} ochre}
+    {color Element {Pb} ochre}
+    {color Element {Pd} ochre}
+    {color Element {Pm} ochre}
+    {color Element {Po} ochre}
+    {color Element {Pr} ochre}
+    {color Element {Pt} ochre}
+    {color Element {Pu} ochre}
+    {color Element {Ra} ochre}
+    {color Element {Rb} ochre}
+    {color Element {Re} ochre}
+    {color Element {Rf} ochre}
+    {color Element {Rg} ochre}
+    {color Element {Rh} ochre}
+    {color Element {Rn} ochre}
+    {color Element {Ru} ochre}
+    {color Element {Sb} ochre}
+    {color Element {Sc} ochre}
+    {color Element {Se} ochre}
+    {color Element {Sg} ochre}
+    {color Element {Si} ochre}
+    {color Element {Sm} ochre}
+    {color Element {Sn} ochre}
+    {color Element {Sr} ochre}
+    {color Element {Ta} ochre}
+    {color Element {Tb} ochre}
+    {color Element {Tc} ochre}
+    {color Element {Te} ochre}
+    {color Element {Th} ochre}
+    {color Element {Ti} ochre}
+    {color Element {Tl} ochre}
+    {color Element {Tm} ochre}
+    {color Element {U} ochre}
+    {color Element {V} ochre}
+    {color Element {W} ochre}
+    {color Element {Xe} ochre}
+    {color Element {Y} ochre}
+    {color Element {Yb} ochre}
+    {color Element {Zr} ochre}
+    {color Resname {DPPC} silver}
+    {color Resname {DOPC} green}
+    {color Resname {CHOL} white}
+    {color Resname {W} pink}
+    {color Resname {POPC} cyan}
+    {color Resname {CDL0} purple}
+    {color Resname {ION} lime}
+    {color Resname {wall} mauve}
+    {color Resname {POPX} ochre}
+    {color Resname {DIPE} iceblue}
+    {color Resname {DPSM} black}
+    {color Resname {PAPC} yellow2}
+    {color Resname {POPE} yellow3}
+    {color Resname {PAPS} green2}
+    {color Resname {PAP6} green3}
+    {color Resname {ACE1} cyan2}
+    {color Resname {CYF} cyan3}
+    {color Resname {ACE2} blue2}
+    {color Resname {CYM} blue3}
+    {color Resname {NMA} violet}
+    {color Resname {GTP} violet2}
+    {color Resname {MG} magenta}
+    {color Resname {HOH} magenta2}
+    {color Chain {X} blue}
+    {color Segname {} blue}
+    {color Conformation {all} blue}
+    {color Molecule {0} blue}
+    {color Molecule {1} red}
+    {color Molecule {2} gray}
+    {color Molecule {3} orange}
+    {color Structure {3_10_Helix} blue}
+    {color Surface {Grasp} gray}
+    {color Labels {Springs} orange}
+    {color Stage {Even} gray}
+    {color Stage {Odd} silver}
+  }
+  foreach colcmd $colorcmds {
+    set val [catch {eval $colcmd}]
+  }
+  color change rgb 0 0.0 0.0 1.0
+  color change rgb 2 0.3499999940395355 0.3499999940395355 0.3499999940395355
+  color change rgb 3 1.0 0.5 0.0
+  color change rgb 4 1.0 1.0 0.0
+  color change rgb 5 0.5 0.5 0.20000000298023224
+  color change rgb 6 0.6000000238418579 0.6000000238418579 0.6000000238418579
+  color change rgb 7 0.0 1.0 0.0
+  color change rgb 9 1.0 0.6000000238418579 0.6000000238418579
+  color change rgb 11 0.6499999761581421 0.0 0.6499999761581421
+  color change rgb 12 0.5 0.8999999761581421 0.4000000059604645
+  color change rgb 13 0.8999999761581421 0.4000000059604645 0.699999988079071
+  color change rgb 14 0.5 0.30000001192092896 0.0
+  color change rgb 15 0.5 0.5 0.75
+  color change rgb 17 0.8799999952316284 0.9700000286102295 0.019999999552965164
+  color change rgb 18 0.550000011920929 0.8999999761581421 0.019999999552965164
+  color change rgb 19 0.0 0.8999999761581421 0.03999999910593033
+  color change rgb 20 0.0 0.8999999761581421 0.5
+  color change rgb 21 0.0 0.8799999952316284 1.0
+  color change rgb 22 0.0 0.7599999904632568 1.0
+  color change rgb 23 0.019999999552965164 0.3799999952316284 0.6700000166893005
+  color change rgb 24 0.009999999776482582 0.03999999910593033 0.9300000071525574
+  color change rgb 25 0.27000001072883606 0.0 0.9800000190734863
+  color change rgb 26 0.44999998807907104 0.0 0.8999999761581421
+  color change rgb 27 0.8999999761581421 0.0 0.8999999761581421
+  color change rgb 28 1.0 0.0 0.6600000262260437
+  color change rgb 29 0.9800000190734863 0.0 0.23000000417232513
+  color change rgb 30 0.8100000023841858 0.0 0.0
+  color change rgb 31 0.8899999856948853 0.3499999940395355 0.0
+  color change rgb 32 0.9599999785423279 0.7200000286102295 0.0
+}
+vmdrestoremycolors
+label textsize 1.0

molecular_vis/workflows/ras-raf-membrane/task_description.txt

@@ -0,0 +1,20 @@
+1. Please load the Martini coarse-grained simulation file from "ras-raf-membrane/data/ras-raf-membrane.gro" into VMD. The simulations has a membrane and a RAS-RAF protein complex.
+
+2. Use VMD to show a zoomed in side view of the membrane and center on the protein with the protein below the membrane.
+For the bilayer only show the PO4 lipids beads and ROH cholesterol bead and color them gray. 
+Also show the protein back bone beads coloring RAS (resid 2 to 187) red and RAF (resid 188 to 329) blue.
+Take a screenshot of the visualization.
+
+3. Analyze the visualization and answer the following questions:
+Q1: Are there any cholesterol head groups in the bilayer center? (yes/no)
+
+Q2: How many lipids are there within 1.5 nm of the RAF protein?
+A. 0
+B. 0-3
+C. 3-5
+D. >5
+
+4. Save your work:
+Save the VMD state as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.vmd".
+Save the screenshot of the visualization as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.png".
+Save the answers to the analysis questions in plain text as "ras-raf-membrane/results/{agent_mode}/answers.txt".

molecular_vis/workflows/ras-raf-membrane/visualization_goals.txt

@@ -0,0 +1,13 @@
+vision:
+1. Camera Position: Is the image centered on a protein complex composed of clearly distinguishable half red RAS and half blue RAF components?
+2. Membrane Placement: Is a lipid bilayer clearly visible above the protein?
+3. Correct Leaflet Ordering: Is the inner leaflet of the bilayer closer to the protein and the outer leaflet positioned farther away?
+
+text:
+1. Q1 correct answer: Yes
+2. Q2 correct answer: C. 3-5
+
+# Q1 reason: quite some gray dots from cholesterol ROH headgroup bead can be seen in the center of the bilayer, so the answer is YES.
+# Q2 reason: if you run the flowing VMD selection command (name PO4 ROH) and within 15 of (index 3457 to 35009 and resid 188 to 329)
+# You will find 4 lipids head group beads, so the answer is C. 3-5 
+# Note here it’s important to only count each lipid once, e.g. either use a single reference bead per lipid or center of mass, also selecting the protein can be tricky as the lipids and water also if resid’s in the 188 to 329 range so either exclude other molecule or sub select only the protein residues