Pymol interface hbond figures

Skill Ling-MD/md-agent-skills/pymol-interface-hbond-figures

Codex/Cursor Agent Skills for GROMACS MD workflows and publication-ready PyMOL figures

Install

npx -y skills add Ling-MD/md-agent-skills --skill pymol-interface-hbond-figures

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Use when creating reusable PyMOL figures for protein-protein or chain-chain interfaces from PDB/MD snapshot files, especially when the user wants only protein kept, water/ions/ligands removed, inter-chain hydrogen-bonding residues shown as sticks, green dashed hydrogen bonds, chain-colored cartoons and labels, MM/PBSA-style blue/orange chain coloring, or a reproducible PML plus rendered PNG for other systems.

SKILL.md

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PyMOL Interface H-Bond Figures

Create publication-style interface hydrogen-bond figures from local PDB snapshots. This skill captures the workflow used for the Fang_Guobing MD snapshots: protein only, chain-colored transparent cartoon, only hydrogen-bonding interface residues as sticks, green dashed H-bonds, readable residue labels, and reproducible output files.

Quick Start

Use PyMOL's bundled Python interpreter on this machine:

& 'C:\Users\dell\Downloads\PyMOL-3.1.6.1_appveyor2641-Win64-portable-py310\PyMOL\python.exe' `
  'C:\Users\dell\.codex\skills\pymol-interface-hbond-figures\scripts\render_interface_hbonds.py' `
  --pdb 'E:\path\to\snapshot_100ns.pdb' `
  --chain-a A `
  --chain-b B

The script writes, by default, next to the input PDB:

<prefix>_interface_hbonds.png
<prefix>_interface_hbonds.pml
<prefix>_interface_hbond_pairs.tsv
<prefix>_interface_hbond_residues.tsv

Workflow

Confirm the interface chains. Default is A and B; override with --chain-a and --chain-b for other systems.
Run scripts/render_interface_hbonds.py with the PDB path and optional output prefix.
Inspect the PNG. If labels are crowded, regenerate with a larger image size, smaller labels, or use the generated PML as the refinement starting point.
Report the PNG/PML/TSV output paths and summarize detected hydrogen-bonding residues.

Style Defaults

Use these defaults unless the user asks otherwise:

Remove everything except polymer.protein.
Cartoon all protein chains with transparency 0.35.
Chain A color: blue #0B7DB3, matching the prior MM/PBSA bar plot style.
Chain B color: orange-yellow #E69F00, matching the prior MM/PBSA bar plot style.
Hydrogen bonds: green #00C71F, dashed.
Show only hydrogen-bond-forming residues as sticks.
Carbon atoms in sticks match their chain cartoon color; hetero atoms keep atomic colors.
Labels show residue name and number, for example ARG142; label color matches the chain.
No explanatory caption or small text in the upper-left corner.

Useful Options

--out-dir 'E:\path\to\figures'
--prefix site1_site2_100ns
--chain-a C --chain-b D
--chain-a-color '#0B7DB3'
--chain-b-color '#E69F00'
--hbond-color '#00C71F'
--cutoff 3.6
--width 3000 --height 2400
--label-size 24
--cartoon-transparency 0.45
--no-ray

Use a larger --width/--height and smaller --label-size when many residues form H-bonds. Use --cutoff cautiously; the default 3.6 Å is intended for donor/acceptor heavy-atom contacts in MD snapshots where hydrogens may be absent. Use --no-ray for a fast preview, then remove it for the final publication-style render.

Refinement Rules

If the first render is not figure-ready:

Rotate or zoom in the generated PML first; keep the residue/hbond selections unchanged unless the user asks for a different scientific definition.
Keep labels close to residues. It is acceptable for labels to cover cartoon, but avoid covering sticks and avoid label-label overlap.
If a user identifies a specific bad label position, edit the generated PML or rerun with a larger canvas before changing the H-bond detection.
If PyMOL finds too few H-bonds, inspect <prefix>_interface_hbond_pairs.tsv; then consider a slightly larger --cutoff only if chemically reasonable.

Reference

Read references/interface-hbond-style.md for the exact visual contract, troubleshooting notes, and the command pattern used in the earlier successful figures.