[PyMOL] pymol autodock plugin

[Daniel S. <ds...@gw...>]

Dear PyMOLers,

there is a new version of the plugin on the web 
(http://wwwuser.gwdg.de/~dseelig/adplugin.html).

It contains a bunch of new features, like:
- setup and execution of complete docking runs
- support for VINA (http://vina.scripps.edu), a great new Autodock spawn
- viewing of Autodock grid maps in PyMOL
- some lightweight virtual screening functionality

So far it's only tested on Linux and by myself so I expect it to be somewhat 
buggy and unstable. Therefore please report bugs.

Cheers,
Daniel



On Thursday 13 August 2009 22:36:14 Warren DeLano wrote:
> Jed,
>
> With the 1.2 release of PyMOL, we have completely switched over to
> Numpy.  So the first thing to try is to replace:
>
> from Numeric import *
>
> # with
>
> from numpy import *
>
> Cheers,
> Warren
>
> > -----Original Message-----
> > From: Jed Goldstone [mailto:jedgold@MIT.EDU]
> > Sent: Thursday, August 13, 2009 1:34 PM
> > To: pym...@li...
> > Subject: [PyMOL] pymol autodock plugin
> >
> > The autodock plugin written by Daniel Seeliger ceased to function
>
> (load)
>
> > when I upgraded to Pymol 1.2r1.
> > Although it is not compatible directly with Autodock 4, it did have
>
> the
>
> > useful functionality of
> > presenting an autodock 'box' that was readily tweakable, so that the
> > parameters could be exported for
> > Autodock Vina. I would LOVE to have this resurrected, but I don't know
> > python - can anybody help with this?
> >
> > The specific failures I got were:
> >
> > File "C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py", line
>
> 16,
>
> > in <module>
> >     from Numeric import *
> > ImportError: No module named Numeric
> > Error: unable to initialize plugin 'autodock'.
> >
> >
> > Any help would be greatly appreciated.
> >
> > Jed
>
> ------------------------------------------------------------------------
> --
>
> > ----
> > Jed Goldstone
> > Research Specialist
> > Woods Hole Oceanographic Institution
> > Redfield 3-52 MS #32
> > Woods Hole, MA  02543
> > http://www.mit.edu/people/jedgold/home.html
> > (508) 685-2253 (cell/home)     (508) 289-4823 (work/WHOI)
>
> ------------------------------------------------------------------------
> --
>
> > ----
> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>
> 30-
>
> > Day
> > trial. Simplify your report design, integration and deployment - and
>
> focus
>
> > on
> > what you do best, core application coding. Discover what's new with
> > Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives:
>
> http://www.mail-archive.com/pym...@li...
>
>
>
>
>
>
> ---------------------------------------------------------------------------
>--- Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> 30-Day trial. Simplify your report design, integration and deployment - and
> focus on what you do best, core application coding. Discover what's new
> with Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Dr. Daniel Seeliger
Computational Biomolecular Dynamics Group
Max-Planck-Institute for Biophysical Chemistry	
Am Fassberg 11
37077 Goettingen, Germany
Tel: +49 551 201 2310
Fax: +49 551 201 2302
email: ds...@gw...
web: http://wwwuser.gwdg.de/~dseelig