From: Jim Nettles (jnettle_at_emory.edu)
Date: Thu Mar 03 2005 - 16:45:44 CST

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