Sean,
 
You can save some time & a lot of memory by loading the file and removing the atoms in a single-line compound statement (with a semicolon after the load statement).
 
load 1E3M.pdb; remove not A-C+F//

Cheers,
Warren
 

From: Sean Law [mailto:magicmen@hotmail.com]
Sent: Tuesday, May 26, 2009 9:10 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Load Selection

Hi PyMOLers,

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.

Sean


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