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Editorial Team
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Asked: 2026-06-08T11:49:43+00:00

I’m new to programming and computer world. I’m trying to study biomolecular simulations with

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I’m new to programming and computer world. I’m trying to study biomolecular simulations with MMTK.

I run it in Windows 7 and I have already installed this software:

  • python-2.5.4
  • numpy-1.6.2-win32-superpack-python2.5
  • netCDF4-0.8.2.win32-py2.5
  • ScientificPython-2.9.0.win32-py2.5
  • MMTK-2.6.0.win32-py2.5
  • pywin32-217.win32-py2.7

When I run this protein.py mmtk sample, all seems to be OK. It show the numbers of 1000 process steps.

But when I run a script with the view method, like this:

from MMTK import *
molecule = Molecule('water')
molecule.view()

Then I get this message:

There is no program associated with ..pdb files, please install a suitable viewer

After searching for some answers on the internet I got this information: “A viewer for PDB files can be defined by the environment variable PDBVIEWER. For showing a PDB file, MMTK will execute a command consisting of the value of this variable followed by a space and the name of the PDB file.” And my doubt is: how define a viewer for PDB files by the environment variable PDBVIEWER? What would be the variable value?
This issue of the environment variables seems to me so simple as the mystery of life’s emergence on Mars. I know how to change it, but I don’t know what to change or when change it. Reading the Wikipedia articles on the subject didn’t help me too much.
So what I’d like to know is: how exactly to modify the system variable in this case? I must add a new variable (PDBVIEWER) or just one more path to an existing variable? What is the value path to PDBVIEWER (should not it be C:\Windows\System32)?

This is my current variable value:

Variable’s name:
Path

Variables’s value:

C:\Program Files (x86)\PC Connectivity Solution\;C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Program Files (x86)\Common Files\Microsoft Shared\Windows Live;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Windows Live\Shared;%PYTHON_HOME%;%PYTHON_HOME%\Scripts;C:\Program Files (x86);C:\Python27\; C:\Python27\Scripts;C:\Python25\DLLs

I also have this Python variable: PYTHON_HOME with this variable’s value: C:\Python27 (though I’m using Python25 with MMTK).

This question may seem trivial to an experienced programmer. But the answer to it can be very useful to others. There is a large number of biologists, biochemists and pharmacists interested in using computational methods to their problems. These professionals do not always have a computer scientist in the vicinity (especially if they are in an underdeveloped country).

Overcoming this initial frustrating phase of bugs and installation problems can be crucial in the scientific career of many people. And the answer to this question will help them.

Thanks in advance.

If this forum is not appropriate for questions of this level, please give me a feedback.

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1 Answer

  1. Editorial Team

    Install VMD, which is recommended by MMTK for visualization, and run 

    import os
os.environ['PDBVIEWER'] = 'C:/Program Files (x86)/University of Illinois/VMD/vmd.exe'

from MMTK import *
molecule = Molecule('water')
molecule.view()
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