I created this document to store the commands I use often in PyMOL, but can’t remember them when I need them.
The default of the fetch command is to download the asymmetric unit from RCSB. If your protein of interest is a dimer or multimer then you need to download the biological assembly.
See the PyMOL wiki entry for fetch, examples 3 and 4. Also see the entry for assembly.
Example code for downloading the biological assembly of 6tof:
fetch 6tof, type=pdb1
spit_states 6tof
Or
set assembly, 1
fetch 6tof, assembly1, async=0
split_states assembly1
An alternative is to use symmetry mates. Here is the PyMOL wiki page for symexp showing how to do that. An example:
# Expand the ''object'' around its ''selection'' by cutoff Angstroms and
# prefix the new objects withs ''prefix''.
symexp prefix, object, selection, cutoff [, segi]
Or
fetch 6tof
symexp mate, 6tof, 6tof, 1
To use symexp, you need to know which of the symmetry mates to keep and which to discard. In other words, you need to know what the biological assembly looks like, which is usually shown on the RCSB page for the protein of interest.
They do not mention this on the PyMOL wiki reinitialize page, but you can run this command using reinit or even rein.