Load the PDB file
• pymol> fetch 1w2i
Hide everything and then show protein cartoon
• PyMOL> hide everything, all
• PyMOL> show cartoon, all
Color the helix, sheet, and loop
• PyMOL> color purple, ss h
• PyMOL> color yellow, ss s
• PyMOL> color green, ss ""
Color chain A and B
• PyMOL> color red, chain A
• PyMOL> color blue, chain B
Create a surface display for chain A
PyMOL> create obj_a, chain A
PyMOL> show surface, obj_a
Color the active site residue
PyMOL> select active, (resi 14-20,38 and chain A)
PyMOL> color yellow, active
PyMOL> turn y, -60; turn x, -20
PyMOL> zoom active
Locate and display the bound formate ion in the active site.
PyMOL> select ligand, active around 3.5 and resn FMT
PyMOL> show sticks, ligand
PyMOL> show spheres, ligand
PyMOL> alter ligand, vdw=0.5
PyMOL> rebuild
PyMOL> set transparency=0.25
8Rendering and output
• PyMOL> bg_color white
• PyMOL> ray
• File -> Save Image
一順溜做下來，你就可以得到如下的圖片