First Run¶

Launch¶

conda activate codemol
python main.py

The Two-Panel Interface¶

codemol opens with a vertically split window:

┌──────────────────────────────────────┐
│                                      │
│          3D Protein Viewer           │
│    (3D renderer)      │
│                                      │
│    Click + drag to rotate            │
│    Scroll to zoom                    │
│    Middle-click + drag to translate  │
│                                      │
├──────────────────────────────────────┤
│ codemol v1.0                         │
│ Type /load <pdb_id> to begin         │
│ > _                                  │
└──────────────────────────────────────┘

Top panel: 3D rendering viewport (no GUI chrome — just the viewer)
Bottom panel: Terminal-style console for commands and output

Load Your First Structure¶

Click on the console and type:

/load 1ake

This fetches adenylate kinase (PDB ID: 1AKE) from the Protein Data Bank and displays it in the viewer.

The console will report:

Loaded 1AKE (3816 atoms, chains: A)

Navigate the Viewer¶

Action	Mouse
Rotate	Left-click + drag
Zoom	Scroll wheel
Translate	Middle-click + drag
Select atom	Left-click on atom

Action	Keyboard
Rotate	`Ctrl`+`Left` / `Ctrl`+`Right`
Camera reset	`/camera orient`

Try a Few Commands¶

/rep cartoon protein        # Show cartoon representation
/color bychain              # Color by chain
/show ligand                # Show ligands
/hide solvent               # Hide water molecules
/camera orient              # Reset camera to fit everything

What's Next¶

Basic Usage — More commands and practical workflows