VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 18 2005 - 12:12:39 CST

Jim,
  I've posted Python library binaries that should work for you here:
http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/

I'm out of town until March 28, but this ought to get you guys started
in the mean time. Help each other out while I'm out of town. :-)

  John

On Thu, Mar 03, 2005 at 05:45:44PM -0500, Jim Nettles wrote:
> Please include the Mac in that discussion. Thanks!
>
> Jim Nettles
>
> On Mar 3, 2005, at 4:22 PM, John Stone wrote:
>
> >
> >Stephane,
> > You'll need to install Python 2.2 libs and Numeric 22.0 to make
> >the IED plugin in VMD happy. I'm planning to post the necessary
> >files and instructions for adding them to an existing VMD 1.8.3
> >distribution shortly...
> >
> > John
> >
> >On Tue, Mar 01, 2005 at 03:54:24PM +0100, Stef wrote:
> >>In latest VMD 1.8.3 there is the Interactive Essential Dynamics plugin
> >>located in /usr/local/lib/vmd/plugins/noarch/python/ied
> >>
> >>I'm trying to load it into vmd :
> >>gopython /usr/local/lib/vmd/plugins/noarch/python/ied/ied.py
> >>
> >>But i'm stuck with this error message :
> >>
> >>vmd > gopython /usr/local/lib/vmd/plugins/noarch/python/ied/ied.py
> >>Info) Text interpreter now Python
> >>Traceback (most recent call last):
> >> File "VMD", line 19, in ?
> >>ImportError: No module named vmdnumpy
> >>
> >>Whereas i have the module numpy on my computer :
> >>/usr/lib/python2.3/site-packages/Numeric/_numpy.so
> >>
> >>My system is Mandrakelinux 10.1 Official with :
> >>
> >>libpython2.3-2.3.4-6.1.101mdk
> >>python-numeric-23.1-2mdk
> >>python-2.3.4-6.1.101mdk
> >>libpython2.3-devel-2.3.4-6.1.101mdk
> >>python-base-2.3.4-6.1.101mdk
> >>python-gtk-0.6.11-6mdk
> >>python-gtk-devel-0.6.11-6mdk
> >>
> >>Could it be that a path is missing ?
> >>While commenting the firsts vmd-specific lines of the program :
> >>line 19 : #import
> >>molecule,vmdcallbacks,vmdnumpy,trans,animate,graphics
> >>line 20 : #import Molecule
> >>
> >>I can get the script running :
> >>[stephane_at_bioinfo ied-2.02]$ python2.3 ied_test.py
> >>
> >>Interactive Essential Dynamics v 2.0 (http://mccammon.ucsd.edu/ied)
> >>Copyright John Mongan <jmongan_at_mccamon.ucsd.edu>, 2003, 2004
> >>
> >>Citation: Interactive Essential Dynamics. John Mongan. Journal of
> >> Computer-Aided Molecular Design. In press.
> >>
> >>This library is provided under the LGPL with ABSOLUTELY NO WARRANTY.
> >>
> >>There is probably one initialisation part missing in gopython, but
> >>i've
> >>not found where as for now.
> >>
> >>Thanks a lot in advance for the help.
> >>
> >>Stéphane Teletchéa
> >>--
> >>http://www.steletch.org
> >>Fingerprint: 1E83 26EE A2F1 87E5 5865 4DBF F2B4 9083 F44C AE88
> >>GPG key @ http://www.steletch.org/article.php3?id_article=13
> >>Mandrakelinux release 10.1 (Official) @ http://www.mandrakesoft.com/
> >>15:36:45 up 7:15, 1 user, load average: 2.27, 1.98, 1.53
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078