VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 15 2004 - 13:45:47 CDT

Jim,
  I've posted a new Mac build that has the VMD code for
Numeric support compiled into the binary. You'll need to
make sure that your Python installation is using Python 2.2.2,
Numeric 22.0, and that your environment variables are properly
set before starting VMD. (on a Mac you'll have to set them in .cshrc
since that's the only way your GUI shell will get them..)
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node143.html

The new test version is posted here:
  ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd/alpha/vmd183a14.dmg

Let us know if this solves the problem getting IED running.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 11, 2004 at 04:28:44PM -0500, John Stone wrote:
>
> Hi,
> I should have a new test Mac build ready by Monday sometime.
> I've got it building already, but I have various other things to test
> before I build a complete distributions on all the platforms.
>
> John
>
> On Fri, Jun 11, 2004 at 04:29:15PM -0400, nettles wrote:
> > 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
>
> --
> 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