| --- |
| license: cc-by-4.0 |
| configs: |
| - config_name: "cullpdb_pc95.0_res0.0-5.0_noBrks_len40-10000_R1.0_Xray+Nmr+EM_d2026_01_26_chains62732" |
| data_files: "curated_csv/subsets/cullpdb_pc95.0_res0.0-5.0_noBrks_len40-10000_R1.0_Xray+Nmr+EM_d2026_01_26_chains62732.csv" |
| --- |
| # PISCES-CulledPDB |
|
|
| Curated protein chain tables from PISCES/CullPDB: one row per chain with sequence and metadata. |
|
|
| **Dataset:** [PRMegathon26/PISCES-CulledPDB](https://huggingface.co/datasets/PRMegathon26/PISCES-CulledPDB) |
|
|
| Use the **subset dropdown** in the viewer to switch between the main table and 242 curation subsets. |
|
|
| ## Summary |
|
|
| | Item | Description | |
| |------|-------------| |
| | **Main CSV** | `curated_csv/cullpdb_compiled.csv` — 4,540,884 chains | |
| | **Subsets** | `curated_csv/subsets/*.csv` — 242 files (same columns) | |
| | **Index** | `curated_csv/cullpdb_list_fasta_index.csv` — 242 rows | |
|
|
| Full list of subset paths: `curated_csv/dataset_metadata.json` (keys `data_paths`, `subset_paths`). |
|
|
| ## Columns (chain CSVs) |
|
|
| | Column | Description | |
| |--------|-------------| |
| | **pdb_chain** | PDB chain ID (e.g. 1ABC_A) | |
| | **pdb** | PDB ID (first 4 chars) | |
| | **chain** | Chain ID | |
| | **sequence** | Amino acid sequence (one-letter) | |
| | **len** | Sequence length | |
| | **method** | Experimental method (e.g. XRAY, NMR) | |
| | **resolution** | Resolution in Å (per structure) | |
| | **rfac** | R-factor | |
| | **freerfac** | Free R-factor | |
| | **pc** | Sequence identity cutoff % used for this subset | |
| | **no_breaks** | Whether chain has no breaks (yes/no) | |
| | **R** | R-factor cutoff used for this subset | |
| | **source_list** | Subset list basename (identifies curation parameters) | |
|
|
| ## Index CSV columns |
|
|
| | Column | Description | |
| |--------|-------------| |
| | **list_basename** | Subset list basename | |
| | **fasta_basename** | Corresponding FASTA basename | |
| | **list_path** | Full path to list file | |
| | **fasta_path** | Full path to FASTA file | |
| | **n_chains** | Number of chains in this subset | |
| | **pc** | Sequence identity cutoff % | |
| | **resolution** | Resolution range (e.g. 0.0-2.0) | |
| | **no_breaks** | yes/no | |
| | **R** | R-factor cutoff | |
| | **Nmethods** | Experiment types (e.g. Xray, Xray+EM) | |
|
|
| ## Usage |
|
|
| ### Python |
|
|
| ```python |
| from huggingface_hub import hf_hub_download |
| import pandas as pd |
| |
| path = hf_hub_download(repo_id="PRMegathon26/PISCES-CulledPDB", filename="curated_csv/cullpdb_compiled.csv", repo_type="dataset") |
| df = pd.read_csv(path) |
| ``` |
|
|
| ### Filter (filter_chains_csv.py) |
|
|
| From repo root after clone/download: |
|
|
| ```bash |
| python src/filter_chains_csv.py --input curated_csv/cullpdb_compiled.csv --output my_filtered.csv --pc 20 --resolution-max 2.0 --no-breaks yes --R 0.25 |
| ``` |
|
|
| Options: `--pc`, `--pc-min`, `--pc-max`, `--resolution-min`, `--resolution-max`, `--no-breaks`, `--R`, `--method`, `--len-min`, `--len-max`. |
|
|
| ## License |
|
|
| cc-by-4.0 |
|
|
