Re: [PyMOL] pymol raytracing crash

2003-09-16 Thread Thomas Siegmund
Dear Warren,

I installed it with python distutils from source. See the bug report I filed 
in the meantime for details. It turned out to be a problem with some versions 
of gcc - crash when raytracing lines, sticks or meshes with gcc (GCC) 3.3 
20030226 (prerelease) (SuSE Linux) and with gcc 3.3.1, but a perfectly 
stable PyMOL with good old gcc 2.95.3.

Best regards

Thomas

Am Dienstag, 16. September 2003 00:37 schrieb Warren L. DeLano:
 Thomas,

   I tried running your script on the current development version
 and on a version 0.90 binary, and wasn't able to get PyMOL to crash.

   How is PyMOL installed on your system?

 Cheers,
 Warren

 --
 mailto:war...@delanoscientific.com
 Warren L. DeLano, Ph.D.
 Principal Scientist
 DeLano Scientific LLC
 Voice (650)-346-1154
 Fax   (650)-593-4020

  -Original Message-
  From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
  ad...@lists.sourceforge.net] On Behalf Of Thomas Siegmund
  Sent: Wednesday, September 10, 2003 6:16 AM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] pymol raytracing crash
 
 
 
  Hi everybody,
 
  I am new to pymol. So maybe I'm doing something wrong, but pymol

 almost

  everytime crashes when I try to raytrace a picture. I had some success
  with
  small protein structures in cartoon representation. The same molecule

 in


-- 
Thomas Siegmund, Ph.D.
DeveloGen AG
Bioinformatics and Data Management
Phone: +49(551) 505 58 651

E-Mails k├Ânnen unvollst




[PyMOL] getting color of a residue + selecting non-natural residues

2003-09-16 Thread Tina Li
Hello,

I have two operations that I want to perform, and am not aware of a simple way
(if possible) of doing them. So here it goes:

1. how (if possible) to retrieve the color for a residue as identified in an
expression, e.g. resi 9? Note that it's not a range so no multiple answers
is possible. I guess the question could extend to other attributes like
representation, etc. The reason I need that is to be able to switch back to a
residue's original color after highlighting it in another.

2. how to select all non-natural residues (anything that's not in the list of
20 standard AAs)?

I'm going the brute-force way, i.e.

naturals1='asp+glu+lys+arg+phe+tyr+cys+met+ser+thr'
naturals2='asn+gln+leu+val+ile+gly+ala+his+trp+pro'
select naturals1, resn naturals1
select naturals2, resn naturals2
select nonnaturals, !naturals1  !naturals2

which is ugly. I couldn't find a predefined keyword for them though.

Many thanks!

Tina