[PyMOL] Plug-in Menu

I am interested in developing some simple plugins for the new release, and I was wondering if there was a document or api specifying how to go about this. As the subject says, for example, how do you add a plugin entry to the new menu bar list. Thanks, Charles Moad Scientific Data Analysis

Re: [PyMOL] Plug-in Menu

ner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | 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

[PyMOL] Adding a viewport

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 actu

[PyMOL] Negative residue index

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] Fast Coloring

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 possib

Re: [PyMOL] Fast Coloring

ists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Charles Moad Sent: Monday, August 23, 2004 5:50 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Fast Coloring I am working on a plugin that entails coloring residues based on a value. Right now creating

Re: [PyMOL] Swissprot

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 Mon,

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

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 eve

Re: [PyMOL] Use API from pymol

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

[PyMOL] Re: Warning: Nvidia 6111 drivers for linux

FYI for people with this problem. The EASIEST solution is the same that people are using for ut2004 and doom3 in linux oddly enough. Just run: LD_PRELOAD=/usr/lib/libGL.so pymol - Charlie

Re: [PyMOL] Coloring gradient

I think I can help you except for one part. In short you want the 'spectrum' command. For example, you can color a chain R, based on the b-factor with the command: spectrum b, green_yellow, chain R The problem is that you must color based on a numeric value that each atom has associated. S

[PyMOL] cmd.read_pdbstr segfault

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] residue selection in one chain only

I use something like: color blue, resi 10-20 and chain R On Fri, 2004-11-19 at 09:57 -0500, A. Thomas Torello wrote: > Hi there, > Sorry to post such a basic question, I'm new to PyMol and am having > trouble mastering some of the basics. > > Suppose I have a pdb file with multiple chains, and

Re: [PyMOL] cmd.read_pdbstr segfault

ow. -Tom -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf Of Charles Moad Sent: Friday, November 19, 2004 5:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] cmd.read_pdbstr segfault pymol-0.97

Re: [PyMOL] cmd.read_pdbstr segfault

(650)-872-0942 Tech:(650)-872-0834 . 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 Thomas Stout Sent: Saturday, November 20, 2004 2:31 PM To: C

RE: [PyMOL] cmd.read_pdbstr segfault

x27;m going to view this as a non-issue. > > > > > > Cheers, > > > Warren > > > > > > -- > > > Warren L. DeLano, Ph.D. > > > Principal Scientist > > > > > > . DeLano Scientific LLC > > > . 400 Oyster Point Blvd., Su

RE: [PyMOL] cmd.read_pdbstr segfault

uth San Francisco, CA 94080 > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > > > -Original Message- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-

[PyMOL] Animated Zoom

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

[PyMOL] Stereo Segmentation fault

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

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

Re: [PyMOL] setting stereo separation distance in pymol

I just posted a script relating to another issue that sets these values. Here it is again. You will probably be interested in the last 3 lines. You can type these commands in pymol like "stereo walleye" and "set stereo_shift, 0.23". - Charlie --

[PyMOL] RE: pdb loader service

> 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 t

Re: [PyMOL] gradient color scheme in pymol

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, diff

[PyMOL] install_plugin(s)

The pymol-0_98-src.tgz download seems to have the following typo: cm...@euclid ~ $ grep -r 'install_plugin' pymol-0.98/ pymol-0.98/modules/pmg_tk/skins/normal/__init__.py: def install_plugins(self): pymol-0.98/modules/pmg_tk/skins/normal/__init__.py: command = lambda s=self: s.install_