[MMTK] MMTK with VMD on Mac OSX

Ryan Bannen rmbannen at wisc.edu
Thu Jul 21 00:40:44 CEST 2005

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:


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 : )




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)
    # 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.)

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