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:magic...@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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