Basic Usage¶

Command Syntax¶

Every command follows this pattern:

/<tool_group> <tool_name> [arg1] [arg2] ...

Most commands have shortcuts so you don't need to type the full group name:

You type	Expands to
`/load 1ake`	`/io load 1ake`
`/rep cartoon protein`	`/representations cartoon protein`
`/color red ligand`	`/color color red ligand`
`/measure distance A/45/CA B/120/CA`	`/measurements distance A/45/CA B/120/CA`
`/show organic`	`/visibility show organic`
`/hide solvent`	`/visibility hide solvent`
`/label ligand`	`/labels smart ligand`

Autocomplete¶

The console supports tab-completion. Start typing a command and press Tab to see available options.

Five Practical Examples¶

1. Visualize a Protein with Ligand¶

/load 4HHB                  # Load hemoglobin
/rep cartoon protein         # Protein as cartoon
/rep sticks organic          # Ligands as sticks
/color bychain               # Color chains differently
/hide solvent                # Remove water clutter
/camera orient               # Frame everything

2. Measure a Distance¶

/load 1ake
/measure distance A/45/CA A/120/CA

The distance appears as a dashed line in the viewer and the value prints in the console.

3. Analyze Interactions¶

/load 3HTB                   # Load a protein-ligand complex
/interactions hbonds          # Find hydrogen bonds
/interactions saltbridges     # Find salt bridges
/interactions summary         # Get interaction summary

4. Compare Two Structures¶

/load 1ake                   # Load open conformation
/load 4ake                   # Load closed conformation
/analysis align 1AKE 4AKE    # Structural alignment
/analysis rmsd 1AKE 4AKE     # Calculate RMSD

5. Create a Publication Figure¶

/load 1ake
/presets publication          # High-quality preset
/color spectrum               # Rainbow coloring
/rendering background white   # White background
/export ray my_figure         # Ray-traced image

Selection Syntax¶

codemol uses a selection syntax with convenient aliases:

Alias	Resolves To	Meaning
`protein`	`polymer.protein`	Protein chains
`ligand`	`organic`	Small-molecule ligands
`solvent`	`solvent`	Water molecules
`metals`	`metals`	Metal ions
`backbone`	`backbone`	Backbone atoms (N, CA, C, O)
`sidechain`	`sidechain`	Side-chain atoms

Chain/residue selections use the chain/residue/atom format:

A/45/CA          # Chain A, residue 45, CA atom
A/45-50          # Chain A, residues 45-50
chain A          # All of chain A
resi 45          # Residue 45 in any chain

Getting Help¶

Type a partial command to see autocomplete suggestions
Check the Command Reference for all available commands
Use /info list to see loaded structures