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

[Bernhard L. <bc...@ca...>]

Hello Santiago,

have you tried using the graphics drivers from the xorg-edgers project?

That helped me with the stick coloring problem:
http://www.mail-archive.com/pym...@li.../msg09210.html

and may also help with your problem.

Bernhard


-----Original Message-----
From: Santi Rios <sri...@gm...>
To: pym...@li...
Subject: [PyMOL] Pymol 1.4.1 problem coloring cartoons. They turn to
black.
Date: Thu, 28 Jul 2011 11:37:56 +0200

Dear Pymol Users,

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).

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).

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.

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

Thanks

Regards,
Santiago

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
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