A curated reference of PyMOL commands for protein structure visualization, organized by task. Covers surface rendering, labeling, ray tracing, colorblind-friendly palettes, and publication-quality figure generation.
Pymol_Comands.Rmd - annotated command reference covering:
Display & Rendering
- Cartoon, stick, and surface representations
- Transparency and surface quality settings
- Ray tracing with configurable resolution (1800x1200)
- Anti-aliasing and shadow control
- Fog for depth perception
Labeling
- Residue and atom labels with custom formatting
- Greek letter support (alpha-helix, beta-sheet Unicode labels)
- Font size, color, outline, and positioning
- Label placement in 3D space
Colorblind-Friendly Palettes
- Pre-defined color scheme (wred, wblue, wgold, wgreen, etc.)
- Ready-to-use setup block for accessible figures
Navigation & Selection
- Selection algebra reference
- Zoom, center, and consistent zoom across multiple structures
Figure Generation
- Complete workflow from display setup to PNG export
- Combined cartoon + surface + labels pipeline
Open Pymol_Comands.Rmd as a reference document. Copy commands into the PyMOL console or script editor as needed.
For the colorblind-friendly figure workflow, copy the full block starting with bg_color white into your PyMOL session.
Sanjiv Kumar - used for structural biology visualization during research on anti-microbial peptides and outer membrane proteins.