I was wondering if there is a way to load part of a PDB file if you know a priori what you want thereby saving time/memory?
Currently, I have a system that is ~160,000 atoms (protein-DNA complex with explicit water molecules taken from an MD simulation). When I load more than 10 structures I start running out of memory so I was hoping that there was some way that I could specify on the command line to only load the protein/DNA but not the water. Right now, I have to pre-process each pdb file before loading which seems tedious. I was hoping that there was already some built-in function in PyMOL that can handle this immediately by invoking something like:
load 1E3M.pdb, selection="c. a+b or c. e+f"
Thank you for your time.
Create a cool, new character for your Windows Live™ Messenger. Check it out