Hi Jason,

Thanks for your prompt reply.

2011/7/28 Jason Vertrees <jason.vertrees@schrodinger.com>

> This only happens if I use the "set use_shaders, 1". If I don't use this
> command, the "cartoon" and "stick" are displayed in the right colour, but
> then I have problems coloring the sticks (it's a known bug :
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09181.html).


The stick coloring bug was fixed not too long ago. Please try pulling
the source code and rebuilding or ask your package maintainer rebuild.


Sorry I am not sure I understand you.

I still have the stick coloring bug. But also now I have a problem with cartoon.

I am using latest Pymol 1.4.1 downloaded from schrodinger website (we're customers). I haven't found any newer source code around, but only a beta.

Which source code you mean ?
 

> Is this a known bug ? Does anybody know what to do ?

What does PyMOL report upon launching? Does it emit any messages about
shaders? For my computer I see:
"""
PyMOL(TM) Incentive Product - PyMOL Executable Build
 Copyright (C) Schrodinger, LLC

 This PyMOL Executable Build is available only to PyMOL Power, Casual, and
 Developer Users who have a valid license to use this software product. Any
 other usage is specifically prohibited and may constitute a violation of
 United States and international copyright laws.

 This Executable Build integrates and extends Open-Source PyMOL 1.5.0.
 Detected OpenGL version 2.0 or greater.  Shaders available.
 Detected GLSL version 1.20.
 Adjusting settings to improve performance for ATI cards.
 Detected 16 CPU cores.  Enabled multithreaded rendering.
"""

So please copy/paste that block from your version of PyMOL.


 This Executable Build integrates and extends Open-Source PyMOL 1.4.1.
 Detected OpenGL version 2.0 or greater.  Shaders available.
 Detected GLSL version 1.20.
 Detected 2 CPU cores.  Enabled multithreaded rendering.



 

> By the way, this is a relevant piece of output of my glxinfo command on
> linux :
> OpenGL vendor string: Tungsten Graphics, Inc
> OpenGL renderer string: Mesa DRI Mobile Intel® GM45 Express Chipset GEM
> 20100330 DEVELOPMENT x86/MMX/SSE2
> OpenGL version string: 2.1 Mesa 7.9-devel

After seeing this, my suggestions are: (1) update your video driver to
the most recent (stable) version; (2) use the latest PyMOL source
code.


(1) I think I am already using the latest stable, but another user suggested using the latest unstable version has fixed it. I am going to give it a try.

(2) As said above, where can I find this latest pymol source ?

Thanks.

Regards

 
Cheers,

-- Jason

--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120