[PyMOL] Bugs squashed in my scripts

2004-04-08 Thread Robert Campbell
Dear PyMOLers,

It was brought to my attention yesterday that 2 of my scripts had
problems with their selection routines, so I've put repaired versions up
on my web site. They are:


The problems arose if you had more than one object up with multiple
chains and tried to colour just one object. I'm not sure how I managed
to miss this bug before! :(

Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-04-08 Thread Michael Banck
On Thu, Feb 19, 2004 at 12:24:53PM +0100, Michael Banck wrote:
 On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
  For me PyMol on SuSE 8.2 crashed always when raytracing a line element. 
 That seems to be identical to Debian Bug #229080
  The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
  got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have not
  tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only)
  solved the problem for me. See PyMol bugreport 806361.
 Thanks for the information, I will see whether that helps on Debian,

For the record, the current gcc-3.3 in Debian testing/unstable seems to
work fine again for rendering sticks and lines, so I uploaded 0.95-1
using the standard gcc on all architectures again.


RE: [PyMOL] color

2004-04-08 Thread Warren DeLano
Yes, it's called spectrum...but it looks like the docs don't exist yet.

PyMOLspectrum ?
Usage: spectrum [ expression [, palette [, selection [, minimum [, maximum
[, byres [, quiet ]]]


spectrum b
spectrum q
spectrum b, selection=my_obj
spectrum b, minimum=5, maximum=60
spectrum count, selection

spectrum b, TAB 

will show you the list of spectra names currently available

spectrum count, red_green



 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Sent: Thursday, April 08, 2004 8:12 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] color
 I have a naïve question here. Is there any command line 
 equivalent to using the menu color the by spectrum (rainbows and etc)?

[PyMOL] Pymol and Matlab

2004-04-08 Thread Zach
Hello to all,

I have created a GUI for a particular application I am
developing in Matlab. I would love to be able to call 
Pymol and operate it from within this GUI.

My GUI does certain calculations on protein based structures and
I do need to visualize the results; in particular, I would
be interested in residue selection and their display over a
cartoon of the protein. Has anyone interfaced Matlab and
Pymol and can give me a push in the right direction to
do this?

I know I could create a script and load it from PyMol but
this would not be the best solution. Is PyMol for Win DDE

Thanks a lot for your help!

Zach Fernandez

[PyMOL] spectrum, util.rainbow

2004-04-08 Thread wgscott

Hi folks:

Why is spectrum and the internal gui (which I assume invokes 
spectrum) so much faster than util.rainbow ?

I like the util.rainbow default color scheme a bit better, but it takes 
forever for large complexes.  Is there a simple way to get spectrum

to mimic the rainbow color scheme?