Hello,
Since it is plugin season, I thought of contributing too. I have a
plugin which is very specific to my research needs in structure based
drug design. It marries the PyMOL interface with other command line
software packages, such as DivCon and AMBER. Both these packages can be
obtained from other sources. AMBER is a popular simulation package from
UCSF. DivCon was developed at the Merz research group at Penn State
and can be obtained from http://www.quantumbioinc.com
I did not write this with the aim to distribute it but just as a way to
learn Python and PyMOL. But my colleagues who have used it, describe it
as useful. So, PyMOL users who have access to these programs might find
it useful too. In addition to the features that use the above programs,
there are other features not dependent on any external programs and
could be helpful during visualization and analysis of biomolecular
structures. Anyway, a short description of the plugin can be found at
the following location from where it can be downloaded too:
http://www.personal.psu.edu/kxr205/research/divscore.html
The introduction to the plugin in the above webpage is pretty ambitious
and was written when the realization that a PhD has to be finished had
not sunk in. But the features that have been described will all work
once the programs are installed correctly. The installation is
straightforward and follows the pymol plugin philosophy. If anybody is
interested and has problems installing it then please e-mail me. As for
platform dependence -- Since it uses external programs such as AMBER
and DivCon, they need to be compiled for the specific platform. I have
tested it out on RedHat Linux and it works fine. The features that do
not need external programs (not too many of them yet) are platform
independent.
I just checked out the sequence viewer in 0.96 and its great.
Kaushik
--
Kaushik Raha
Merz Research Group
Penn State University
On Wednesday, July 14, 2004, at 03:56 PM, Warren DeLano wrote:
Charles,
Simply awesome! It works great on Windows and Mac too...
Folks, I think we've finally hit on a workable paradigm for extending
PyMOL's capabilities via these lightweight, end-user-installable
plugins.
You have my full encouragement -- go crazy with this stuff! This
grass-roots user-driven development is exactly what PyMOL was supposed
to
enable...
To help the sharing process along, I've created a new plugins page on
the
SourceForge site and welcome your submissions.
http://pymol.sf.net/plugins.html
I can already see that we'll need a user-friendly "Install Plugin..."
menu
item in the next release that will automatically copy plugin files to
the
correct location. In the meantime, installation directions can be
found on
that page...
Provided that plugins are released under a suitable (non-viral)
open-source
license, I don't see any reason why good ones couldn't become part of
the
standard PyMOL distribution, which would of course save users the
trouble of
having to download and install them.
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Charles Moad
Sent: Wednesday, July 14, 2004 11:32 AM
To: Michael George Lerner
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Plug-in Menu
Thanks for the info. Using your APBS as an example I
made a very simple remote pdb loader. You can check it out
at "http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/"; or
download it directly from
"http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/remote_pdb_load.py";.
It is inspired from chimera's remote pdb loading feature.
Thanks again,
- Charlie
Michael George Lerner wrote:
Hi,
There's some example code in
pymol/modules/pmg_tk/startup/__init__.py.
You can see how it works by copying it (uncommented) into a
new file
and placing that file in pymol/modules/pmg_tk/startup.
You'll see the
new plugins the next time you start PyMOL. I have a larger plugin
that I've written .. I'll be sending out an announcement
about it later today.
-michael
--
This isn't a democracy;| _ |Michael Lerner
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 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 Lab
Indiana University
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