Re: [PyMOL] gradient color scheme in pymol

2005-05-06 Thread Charles Moad
set_color salmon, [1.0, 0.8, 0.8] color salmon, all Bingding Huang wrote: Another question, Is it possible to use RGB color in pymol like color [0,128,255], resn CYS ? I tried it but it failed in pymol! Thanks? Is there any gradient color scheme in pymol? i.e, different residues

[PyMOL] RE: pdb loader service

2005-03-24 Thread Charles Moad
is it possible to use the pdb loader in a *.pml style script? With the shipped plugin it may be hard. I wrote the original, but have since written a new/improved one that does not tough the filesystem and adds a remote command that will fetch and load pdbs as well. You can see the code for

[PyMOL] Stereo Segmentation fault

2005-02-09 Thread Charles Moad
The CVS version in linux seg faults when trying to launch this simple stereo startup script. I get this on two very different linux distros and dependency versions. #!/usr/bin/env python # Tell PyMOL we don't want any GUI features. import __main__ __main__.pymol_argv = [ 'pymol', '-Gi' ] #

Re: [PyMOL] Stereo Segmentation fault

2005-02-09 Thread Charles Moad
Follow up to this. At least on one machine of the machines mentioned, this script works fine when I copy/paste each line into idle. Strange Charles Moad wrote: The CVS version in linux seg faults when trying to launch this simple stereo startup script. I get this on two very different

[PyMOL] Animated Zoom

2005-02-08 Thread Charles Moad
Can the cmd.zoom func be used to gain access to the animated zoom? Is there any way to utilize this from a script? Thanks, Charlie

RE: [PyMOL] cmd.read_pdbstr segfault

2004-11-22 Thread Charles Moad
-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Charles Moad Sent: Saturday, November 20, 2004 3:06 PM

[PyMOL] cmd.read_pdbstr segfault

2004-11-19 Thread Charles Moad
pymol-0.97 cmd.read_pdbstr is dieing for remotely large pdb files. One for example is 1DT7. I don't get a descriptive error: /usr/local/bin/pymol: line 2: 10486 Segmentation fault /usr/bin/python /usr/local/lib/python2.3/site-packages/pymol/__init__.py $* Thanks, Charlie

Re: [PyMOL] pymol and Desktop Manager on OS X

2004-10-26 Thread Charles Moad
Have you tried pymol -G for game mode? On Tue, 2004-10-26 at 00:33, Jianghai Zhu wrote: Hi, all, Anybody has any experiences of using full-screen pymol and desktop manager at the same time on OS X? When I am running desktop manager and put pymol into full screen mode, I found every

Re: [PyMOL] Swissprot

2004-10-18 Thread Charles Moad
I think you want to avoid the c files. Look at the pdb loader plugin I wrote: http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/remote_pdb_load.py Specifically, one clean way to load a pdb is: cmd.read_pdbstr(pdbString, label) There is also a command for loading from a file. - Charlie On

[PyMOL] Fast Coloring

2004-08-23 Thread Charles Moad
I am working on a plugin that entails coloring residues based on a value. Right now creating a new color for each residue and setting the color corresponding works, BUT it is very inefficient and takes more than a tolerable amount of time to display. Is there a better approach? It is

[PyMOL] Negative residue index

2004-08-19 Thread Charles Moad
I have only tried this one one pdb, but I opened 1HOZ and the following command throws an error: select 1HOZ and chain A and resi -1 I assume it is the negative number. Is this a bug??? Thanks, Charlie Scientific Data Analysis Lab Indiana University

[PyMOL] Adding a viewport

2004-07-22 Thread Charles Moad
I am assuming a new viewport is added to the main window when the sequence viewer is displayed. This brings up the question, how possible would it be to create a plugin that creates yet another viewport in the main window? Where would I look in the code to do this, or would this require

Re: [PyMOL] Plug-in Menu

2004-07-14 Thread Charles Moad
( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Wed, 14 Jul 2004, Charles Moad wrote: I am interested in developing some simple plugins for the new release, and I was wondering