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

[Santi R. <sri...@gm...>]

Hi Bernhard,

I just installed this new driver :
xserver-xorg-video-intel_2.13.901-2ubuntu2~xup~maverick_i386.deb

And the problem remains the same. Also tried installing the combo of :

libdrm-intel1_2.4.23+git20110119.550fe2ca-0ubuntu0sarvatt~maverick_i386.deb
xserver-xorg-video-intel_2.14.0+git20110220.9599fde6-0ubuntu0sarvatt~maverick_i386.deb

And no luck either.

Which Ubuntu version are you using, 10.10 or 11.04 ?

Also, could you please tell me exactly which driver version are you using ?
Or how did you install them, so I can follow your steps.

Thanks


2011/7/28 Bernhard Lechtenberg <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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