[MMTK] Normal Modes: problem with elastic network example

Konrad Hinsen research at khinsen.fastmail.net
Wed Dec 22 08:38:00 UTC 2010

On 21 Dec 2010, at 15:45, Peter Ebert wrote:

> I am new to the MMTK package (2.7.2) and experience some problems  
> when I try to run the example script "Fast normal modes for large  
> proteins using an elastic network model". I'd like to use VMD as  
> visualization tool (installation of VMD passed without any problems  
> and it runs flawlessly), hence I added two lines to the example  
> script right before the "view(modes[6],15.)" statement:
> definePDBViewer('vmd','/usr/local/bin')
> defineVRMLiewer('vmd','/usr/local/bin')
> I don't know if both are actually necessary but without them, I get  
> the "No viewer defined" message ;-)

The second line doesn't make any difference unless you request VRML  
output. Since VMD is not a VRML viewer, it won't do any good even if  
you do.

To remove the need for the first line, assuming that you are in a Unix  
environment, set the environment variable "PDBVIEWER" to "/usr/local/ 

If you do want to keep the definition of the PDB viewer in script  
itself, make it



>  File "/usr/lib/python2.6/subprocess.py", line 623, in __init__
>    errread, errwrite)
>  File "/usr/lib/python2.6/subprocess.py", line 1141, in _execute_child
>    raise child_exception
> OSError: [Errno 13] Permission denied

... MMTK will try to execute '/usr/local/bin', leading to the error  
message you see.

> It appears to me that there is a problem with some read/write  
> permissions, but running the script as root doesn't change
> that - that puzzles me.

You are trying to execute a directory, which even "root" is not able  
to do!

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net

More information about the mmtk mailing list