From: Jim Nettles (jnettle_at_emory.edu)
Date: Fri Mar 18 2005 - 12:17:25 CST

Thanks John!

I'll try it later today. Your timing is perfect.

Have a great trip.

Jim N.

________________________________________________________
Jim Nettles, Molecular Pharmacology
Liotta/Snyder Group, Modeling Division, Department of Chemistry
Emory University 1515 Pierce Dr. Atlanta, Ga. 30322
jnettle_at_emory.edu TEL: (404)966-4617 FAX: (404)728-0991
________________________________________________________

On Mar 18, 2005, at 1:12 PM, John Stone wrote:

>
> 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