VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 04 2005 - 00:58:24 CST

Jim,
  I plan to post the necessary files for all platforms, though I believe
I remember IED triggered a stability problem with Python and TkInter on
the Mac when shutting down VMD (could crash rather than shutdown cleanly).
We can revisit this once I've got the files posted.

  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