[MMTK] MMTK with VMD on Mac OSX

Vasisht R. Tadigotla vasisht at eden.rutgers.edu
Thu Jul 21 01:55:57 CEST 2005


Hi,

Have you set the PDBVIEWER variable in environment.plist ? This file
should be present in your home directory in the .MacOSX directory. You'll
probably have to create the directory and then create the file in it using
the property list editor.

See instructions in the README file, in the section "Using VMD for
visualization under MacOS X"

Also look at the thread "Visualization with VMD" in the archives.

http://starship.python.net/pipermail/mmtk/2005/000832.html

HTH,
Vasisht




On Wed, 20 Jul 2005, Ryan Bannen wrote:

> Greetings to the readers of the MMTK list,
>
> I'm trying to get MMTK to communicate properly with VMD when running scripts
> on a Mac OSX computer.  I can get VMD running happily by typing
>
>       /usr/local/bin/vmd somepdbfile.pdb
>
> and can run MMTK scripts that do not require the "view" command from the
> console window by typing the filename of the python script.  This leads me to
> believe that both programs are properly installed.
>
> I think that the $PDBVIEWER variable is pointing to the right VMD executable
> file.  For example when i type:
>
>       echo $PDBVIEWER
>
> it returns the following:
>
>       /Applications/VMD_1.8.2/VMD_1.8.2.app/Contents/vmd/vmd_MACOSX
>
> I'm using "fastnm.py" as my script to test the installation.  (I've pasted the
> code at the end of this email).  Everything seems to run properly through the
> two writeToFile commands.  However, when the script tries to run the
> "view(modes[6], 10.)" command, the following is output to the console:
>
>       Warning: No viewer with animation feature defined.
>
> I'm at a loss for how to fix this problem.  I would think that it's some
> simple fix in some configuration file, but I wouldn't know where to start
> looking.  Help from anyone would be greatly appreciated : )
>
> Thanks!
>
> ryan.
>
> ================fastnm.py====================
> #!/usr/local/bin/python
>
> from MMTK import *
> from MMTK.Proteins import Protein
> from MMTK.ForceFields import DeformationForceField
> from MMTK.FourierBasis import FourierBasis, estimateCutoff
> from MMTK.NormalModes import NormalModes, SubspaceNormalModes
> from MMTK.Visualization import view
>
> universe = InfiniteUniverse(DeformationForceField())
> universe.protein = Protein('/Users/badmin/Desktop/1iro.pdb', model='calpha')
>
> # Find a reasonable basis set size and cutoff
> nbasis = max(10, universe.numberOfAtoms()/8)
> cutoff, nbasis = estimateCutoff(universe, nbasis)
>
> print "Calculating %d low-frequency modes." % nbasis
>
> if cutoff is None:
>     # Do full normal mode calculation
>     modes = NormalModes(universe)
> else:
>     # Do subspace mode calculation with Fourier basis
>     subspace = FourierBasis(universe, cutoff)
>     modes = SubspaceNormalModes(universe, subspace)
>
> conf = universe.configuration()
> scale = 15.
> for n in [6]:
>   universe.writeToFile('mode%d_plus.pdb' % n, conf+scale*modes[6])
>   universe.writeToFile('mode%d_minus.pdb' % n, conf-scale*modes[6])
>
> view(modes[6], 10.)
> ==========================================
>
> _______________________________________________
> mmtk maillist  -  mmtk at starship.python.net
> http://starship.python.net/mailman/listinfo/mmtk
>

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