Re: [PyMOL] Pymol 1.4.1 problem coloring cartoons. They turn to black.

[Jason V. <jas...@sc...>]

Hi Santiago,

> I've found a problem with Pymol version 1.4.1. I am using Ubuntu 10.10 in a
> laptop with Intel Mobile 4 graphics controller.
>
> The problem comes when I load any PDB file, then try to show it as a
> cartoon. It displays the cartoon but in black color, so I cannot see it
> unless I turn the background to white. With "lines" it's correctly displayed
> but "cartoon" or "sticks" show the same behaviour (colored black).

There was an older Linux bug that caused PyMOL to improperly
initialize shaders on some systems. There are also driver issues with
the Intel Mobile GMx45 cards.


> 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/pym...@li.../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.


> I don't know if this is related but immediately after loading the pdb I get
> this message in the pymol console :
> PyMOL>load FILE.pdb
>  ObjectMoleculeGuessValences(
> 1,1): Unreasonable connectivity in heteroatom,
>   unsuccessful in guessing valences.

This message is unrelated.


> 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.


> 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.

Cheers,

-- Jason

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

(e) Jas...@sc...
(o) +1 (603) 374-7120