pymol_tricks.md

Some useful colors

• niobium - turqouise-like
• smudge - pale green
• wheat - tan

Display biological unit

To display the biological unit for the PDB structure, the split_state command is used.

split_state myPdbCode

Cartoon Representation

Dealing with fiddling with aesthetics for cartoon representations in pymol can be tricky. Many of the parameters effect the entire structure, but often things need to differ by chain. The solution is to create a new object and set properities for it, rather than trying to use a select statement, which won't work.

load new_obj.pdb

# make the chain into a separate object
create new_obj, chain A
remove mol_obj in new_obj

Now properities can be set for that individual chain.

set cartoon_transparency, .5, new_obj
set cartoon_color, wheat, new_obj