Python MMTK "There is no program associated with ..pdb files, please install a suitable viewer"
Question: 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](http://structure.usc.edu/mmtk/Examples/MolecularDynamics/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.


Answer: Google says <http://spdbv.vital-it.ch/> is a PDB viewer.

You need to install that or something else you find that can view PDB files.
Assuming the installer for that doesn't just go set that environment variable
for you (which it may), you'd then need to set the variable PDBVIEWER to be
the path to an executable that can view PDBs presumably. So, say,
C:\SwissPDBViewer\view.exe hypothetically speaking.

