protein-struct-viz

Generate PyMOL scripts to highlight specific protein residues in PDB structures. Use this skill when the user needs to visualize specific amino acid residues, create publication-quality protein images, or highlight functional sites in protein structures.

Install with Tessl CLI

npx tessl i github:aipoch/medical-research-skills --skill protein-struct-viz

What are skills?

Review — 67%

Does it follow best practices?

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npx tessl skill review --optimize ./path/to/skill

Learn more

Validation — 10 / 11 Passed

Validation for skill structure

SKILL.md

Review

Evals

Evaluation results

100%

Enzyme Active Site Visualization

Basic PyMOL script generation via main.py

Criteria

Without context

With context

Uses main.py script

100%

Correct --pdb argument

100%

Residue spec format

100%

Output filename flag

100%

Output file is .pml

100%

fetch command in script

100%

White background setting

100%

Antialias setting

100%

Hide then show cartoon

100%

Per-residue selections

100%

View centering

100%

Sticks style used

100%

Without context: $0.2547 · 1m 2s · 13 turns · 18 in / 4,271 out tokens

With context: $0.5214 · 1m 33s · 29 turns · 69 in / 4,811 out tokens

100%

Publication-Quality Protein Figure for Journal Submission

Publication-quality ray tracing settings

Criteria

Without context

With context

Uses main.py script

100%

Ray trace flag used

100%

ray_trace_mode 1

100%

ray_trace_gain 0.01

100%

Ray resolution 2400x2400

100%

Antialias 2 setting

100%

White background

100%

fetch for PDB ID

100%

Global cartoon representation

100%

Spheres style

100%

Correct output file

100%

Without context: $0.2922 · 1m 13s · 13 turns · 18 in / 4,588 out tokens

With context: $0.4813 · 1m 30s · 26 turns · 30 in / 4,967 out tokens

100%

Protein-Protein Interface Visualization

Chain-specific residue highlighting and color schemes

Criteria

Without context

With context

Uses main.py script

100%

Chain-specific residue format

100%

Multiple residues comma-separated

100%

Named color scheme used

100%

Chain color scheme in script

100%

Per-residue selections numbered

100%

Per-residue show commands

100%

Per-residue color cycling

100%

fetch for PDB ID

100%

View centering on selections

100%

Output named correctly

100%

Without context: $0.3121 · 1m 50s · 14 turns · 18 in / 5,814 out tokens

With context: $0.4563 · 1m 34s · 23 turns · 29 in / 5,241 out tokens

Evaluated: about 11 hours ago
Agent: Claude Code

Table of Contents

Enzyme Active Site Visualization Publication-Quality Protein Figure for Journal Submission Protein-Protein Interface Visualization

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