VMD-L Mailing List

From: nettles (jnettle_at_emory.edu)
Date: Fri Jun 11 2004 - 15:29:15 CDT

Thank you!!

Matt and I have both been working on this too and had narrowed it down
to something in the Mac-VMD build, but neither have had the time to go
through the source. We were going to write you later today.

I will be happy to test the new build with whatever python you have
linked. ( I would guess 23 at this point) I am really looking forward
to having this running on my Powerbook, so that I can take it on the
road. Much appreciation for the powerful and beautiful tools you have
both given us to display these complex data sets.

With regard,

Jim Nettles

On Jun 11, 2004, at 3:33 PM, John Stone wrote:

>
> Hi,
> I did a little digging and the two causes of this problem are:
> 1) The MacOS X versions of VMD haven't had the NUMPY flag enabled in
> their builds yet.
> 2) Its possible that you've got mismatched versions of python
> libraries,
> but given the subsequent tests you did for me I think that the
> remaining
> issues are likely caused by 1).
>
> I'm doing new Mac builds today that have the NUMPY build option
> enabled,
> and if all goes well I may have a test version of VMD 1.8.3 for you to
> try
> out with John Mongan's IED 2.0.
>
> As it turns out the Mac was the only platform not compiled with the
> NUMPY flag. In some old version of Python/MacOS X we had problems of
> some sort which is the reason, but I think they were resolved with
> more recent revs of Python and VMD so we'll try turning it on and see
> if IED is happy with a new build. I'll let you guys know when I've
> got a new Mac build for you to try with IED 2.0.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jun 03, 2004 at 07:02:19PM -0400, nettles wrote:
>> Hello all,
>>
>> We have been playing back some essential dynamics trajectories on our
>> Linux box at the lab in VMD using the nice piece of code written by
>> John Mongan. http://mccammon.ucsd.edu/ied/
>>
>> I'm running into a problem on my Mac running OSX 10.3.4 and VMD
>> 1.8.2.
>>
>> This is the error.
>>
>> vmd > gopython /Users/nettles/Data/EssDyn/ied-2.0/ied.py
>> Info) Text interpreter now Python
>> Traceback (most recent call last):
>> File "VMD", line 19, in ?
>> ImportError: No module named vmdnumpy
>> Info) Text interpreter now Tcl
>> vmd >
>>
>>
>> I have Python and NumPy installed via Fink. Any clues?
>>
>>
>> Thanks,
>>
>>
>> Jim Nettles
>
> --
> 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