[PyMOL] Downgrading nvidia drivers on linux to v.6629 - suggestion

[Kevin Gardner]

Hi all:
We've definitely seen that pymol incompatibilities with the
nvidia 7-series drivers on FC3 machines in my group.  It's clearly
platform dependent, consistent with some of the other comments provided
here.  For those looking to downgrade back to nvidia's 6629 driver,
it's worth noting that this does not compile on some of the newer
kernels (e.g. FC3 2.6.11-1.14 here), complicating their installation.
This can be handled with a fairly easy patch, well-described at:

http://www.nvnews.net/vbulletin/showthread.php?t=46676

We're nicely back in business after this step --- hope this might
be of use to some of you as well.

Sincerely,
Kevin

--
**
Kevin Gardner, Ph.D.  kevin.gard...@utsouthwestern.edu
Associate Professor - Dept. of Biochemistry - UT Southwestern Med Ctr
214-645-6365/FAX: -6353  http://freedom7.swmed.edu

[PyMOL] Re: hardware stereo in IRIX

[Dr. Daniel James White PhD]

Hi Nicolas,

I have the same SGI computer, Indigo 2 Impact 1
running IRIX 6.5.22m (BTW upgrade to this release is free from 
supportfolio at SGI, might have to install patch 5086 first)


I have stereo graphics emitter and glasses,
and stereo works fine,
i just double click a link on my desktop to pymol.com
pymol version 0.97.

then on menus bar
Display-Stero mode- quad buffered.

running at 1024x786_96s is display settings
on SGI grey speckled monitor.

Are all the cables connected properly for the emitter box?

Dan



On 23 Apr 2005, at 06:19, pymol-users-requ...@lists.sourceforge.net 
wrote:



Hello PYMOLers,
=20
I've recently installed Pymol v0.97 on an SGI but the hardware=20
stereo mode was not detected. Is there somebody successfully using 
PyMol=20
with this mode on an SGI ? If yes, could you please help me to fix 
this=20

problem?
=20
My SGI:
- Irix 64 Release 6.5
- Model Indigo 2 Impact 1
- Main Mem: 128 MB
- CPU: 175 MHz
=20
Thanks a lot,
=20
Nicolas Ambert.

--=20

Dr. Daniel James White BSc. (Hons.) PhD
Bioimaging Coordinator
Nanoscience Centre and
Department of Biological and Environmental science
Division of Molecular Recognition
Ambiotica C242
PO Box  35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)

http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi

[PyMOL] dotted line representation

[Sona Vasudevan]

Hi!

Is there a way in pymol to represent superposition  of two molecules
one as a stick and the other as a dotted line? The purpose is to show
a conformational change.

(mol 1 as sticks and mol2 as dotted lines).

Thanks!

Sona