Hi Scott,
Thanks for that info. That's what i've been doing. (taken from the manual)
Maybe I didn't word my question right. I have several proteins (like 15-20) that i need to do this for and i also have these lists. i was wanting to see if there was anyway to have pymol read in that list automatically so i didn't have to type in all the residues (ie, about 60 on each protein).
thanks though,
-----Original Message-----
From: pymol-users-admin@lists.sourceforge.net [mailto:pymol-users-admin@lists.sourceforge.net] On Behalf Of Scott Classen
Sent: Wednesday, December 03, 2003 3:13 PM
To: <gsk@neo.tamu.edu>; pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selecting a lot of residues

Hi Gwen,
You should really read the manual. Many of these basic questions can be answered by a few minutes of careful reading.

One way of doing what you want to do is to make a small script (we will call it script.pml) that loads your PDB and then creates a selection containing all your residues of interest.

This is script.pml:

load your.pdb, foo
create interestingstuff, ((/foo//A/27,28,141,144,148)
show sticks, interestingstuff

read this into PyMOL by typing:

this would display residues 27,28,141,144, and 148 of chain A of your molecule foo.
You need to become familiar with the various atom selection schemas available in PyMOL to put this to best use for yuor particular PDB.


On Dec 3, 2003, at 12:52 PM, Gwendowlyn S. Knapp wrote:

Hello everyone:
Please excuse this question if it is answered elsewhere. 

I have a structure that I would like to highlight a lot of residues with  a different color and have in a spacefilling mode.  These residues are listed in another (text) file.  I've been doing the selection manually, but was wondering if there was anyway to automate this process at all, ie, using the text file and some sort of import control. 

Any ideas/directions would be appreciated.

Thanks in advacne,

Gwendowlyn S. Knapp
Department of Biochemistry and Biophysics
Texas A&M University
College Station, TX 77843-2128

Scott Classen, Ph.D.
ACS Postdoctoral Fellow
Department of Molecular & Cell Biology
University of California, Berkeley
237 Hildebrand Hall #3206
Berkeley, CA 94720-3206
LAB 510.643.9491
FAX 510.643.9290