---
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