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_
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
> 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
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
--
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
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' ]
#
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
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-
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
(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
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
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
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
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
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
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
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
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,
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
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
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
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
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
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
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