Command Reference¶
Complete reference for all codemol commands, organized by tool group.
Command Syntax¶
Most commands have shortcuts — see each section for details.
Categories¶
| Category | Shortcut | Tools |
|---|---|---|
| IO | /load, /clear |
load, clear, density, project |
| Representations | /rep |
cartoon, sticks, surface, spacefill, ... |
| Color | /color |
bychain, byelement, spectrum, color, ... |
| Measurements | /measure |
distance, angle, dihedral, contacts, ... |
| Analysis | — | align, rmsd, clashes, pockets, ... |
| Interactions | — | hbonds, saltbridges, pistacking, ... |
| Labels | /label |
label, smart, font, color, ... |
| Visibility | /show, /hide |
show, hide |
| Surface | — | area, transparency, type |
| Camera | — | orient, zoom, turn, clip |
| Presets | — | publication, presentation, pretty, ... |
| Edit | — | hadd, remove, alter, extract, ... |
| Session | — | save, load, list, update, delete |
| Docking | — | load, info, cluster, split, ... |
| Trajectory | /traj |
load, play, rmsd, align, ... |
| Sharing & Agents | /share, /agents |
create, join, use, list, ... |