Re: [PyMOL] Use API from pymol

2004-11-01 Thread Charles Moad

I believe it is "pymol -c "

Try "help launching" from within pymol to see all the startup flags.

- Charlie

On Nov 1, 2004, at 5:38 PM, j...@fis.unam.mx wrote:



Hi

How Can I use only  Pymol's APIs  within a standalone
Python script, But I don't want display The Pymol's GUI yet?

thanks a lot

  Javier


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[PyMOL] Use API from pymol

2004-11-01 Thread jrm
Hi

How Can I use only  Pymol's APIs  within a standalone
Python script, But I don't want display The Pymol's GUI yet?

thanks a lot

  Javier



RE: [PyMOL] stereo projection with PyMOL

2004-11-01 Thread EPF (Esben Peter Friis)
Hi Seth

First, I don't think it is possible at all to create shutter-glass
stereo on a standard DLP or LCD projector. I have actually tried this
(using an SGI) by going to very low refresh rates, such as 2x30 Hz. I
got some kind of effect, but the DLP/LCD projector does not sync
correctly to the refresh from the video card. So, the effect was on/off
every 10 seconds. 
It is hard to tweak the refresh rate of the SGI video card, but it is
possible. I can probably dig out my old files if you like, but I don't
think it is worth trying

You can only reliably do this kind of stereo with a fast CRT projector,
which are sold by eg. Barco. If you want to use the SGI, you can either
stick to the CRT-projector and shutter glasses OR buy a stereo-splitter
box ($10,000) and set up a polarized two projector solution (see below).
   
We have great succes with PyMOL stereo on a two-projector system:
 - A Linux box with a Nvidia Quadro card provides the graphics (around
$2000)
 - Two standard DLP projectors ($1500 each)  
 - 2 Circular polarized filters ($300 total)
 - 30 Plastic circular polarized glassed ($375)
 - Projector stand and filter holder (about $700)
 - Non depolarizing screen ($2000) 
(prices just from memory :-)

So you can be running for less than $9000 (even less if you go for a
cheaper screen and a linear polarized solution). I doubt that you can
get a decent CRT projector for that kind of money :-) The equipment was
bought from REASOM (http://www.reasonco.com) and ProjectorPoint
(http://www.projectorpoint.com).

This 3D projection system is a real showoff, both internally and for
costumer/guest presentations! 


Best regards

Esben

-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Seth
Harris
Sent: 1. november 2004 20:16
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] stereo projection with PyMOL



I was curious if anyone has successfully done stereo over 
a projector with PyMOL.  That is to say not the cross-eyed 
stuff but the shutter-glasses type stereo. I was recently 
trying to do this for a company presentation from an SGI. 
 On the same machine Insight can do stereo (although they 
tell me it took some fiddling), and while PyMOL goes into 
stereo mode on the monitor, the projected image only shows 
one of the eye views.  Both programs have stereo within a 
window so I didn't think it was a fundamental difference 
in the overall mode, but perhaps a difference in their 
chosen frequencies.  If this turns out to be the case, is 
it possible to change the frequency PyMOL uses for 
shuttered stereo such that I could sync it with the 
projector's presumably more limited range?

Thanks,
seth


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[PyMOL] stereo projection with PyMOL

2004-11-01 Thread Seth Harris
I was curious if anyone has successfully done stereo over 
a projector with PyMOL.  That is to say not the cross-eyed 
stuff but the shutter-glasses type stereo. I was recently 
trying to do this for a company presentation from an SGI. 
On the same machine Insight can do stereo (although they 
tell me it took some fiddling), and while PyMOL goes into 
stereo mode on the monitor, the projected image only shows 
one of the eye views.  Both programs have stereo within a 
window so I didn't think it was a fundamental difference 
in the overall mode, but perhaps a difference in their 
chosen frequencies.  If this turns out to be the case, is 
it possible to change the frequency PyMOL uses for 
shuttered stereo such that I could sync it with the 
projector's presumably more limited range?


Thanks,
seth



[PyMOL] ribbon view of c-alpha only coordinates

2004-11-01 Thread Cathy Lawson

Dear Fellow Pymolers,

Some PDB files (notably models fitted into EM density) contain only C-alpha 
coordinates.
When read into Pymol, Ive found that the coordinates appear as a 
constellation of individual atoms, and selecting a ribbon view doesn't 
connect them with lines.


Anyone know a workaround to view C-alpha atom coordinates in Pymol as 
C-alpha traces?


thanks,

Cathy Lawson




***
Catherine L. Lawson
Laboratory for Structural Biology and Bioinformatics
Department of Chemistry and Chemical Biology
Rutgers University
610 Taylor Road, Piscataway, NJ 08854
cathy.law...@rutgers.edu
tel 732 445 8074
fax 732 445 5312
http://rutchem.rutgers.edu/~lawson
http://roma.rutgers.edu/~lsbb
*