[MMTK] Normal Modes: problem with elastic network example

Peter Ebert s9preber at stud.uni-saarland.de
Tue Dec 21 14:45:02 UTC 2010


Hi,
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 ;-)

Running the script leads to the following output:

pepeg at Pegasus:~/Py_NMA$ python test_NMA.py
Calculating 24 low-frequency modes.
Traceback (most recent call last):
   File "test_NMA.py", line 40, in <module>
     view(modes[6], 15.)
   File  
"/usr/local/lib/python2.6/dist-packages/MMTK/Visualization.py", line  
196, in view
     object.view(*parameters)
   File  
"/usr/local/lib/python2.6/dist-packages/MMTK/NormalModes/Core.py",  
line 102, in view
     Visualization.viewMode(self, factor, subset)
   File  
"/usr/local/lib/python2.6/dist-packages/MMTK/Visualization.py", line  
332, in viewMode
     label)
   File  
"/usr/local/lib/python2.6/dist-packages/MMTK/Visualization.py", line  
290, in viewSequence
     function(object, conf_list, periodic, label)
   File  
"/usr/local/lib/python2.6/dist-packages/MMTK/Visualization.py", line  
501, in viewSequenceVMD
     subprocess.Popen([viewer['pdb'][1], '-nt', '-e', script])
   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

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. So, I'm not sure if the above mentioned statements to  
define the viewer are correct (for the case of normal mode  
calculations) or if I have to change some read/write permissions (but  
read permission is set for /usr/local/lib/python2.6/dist-packages as  
well as for /usr/lib/python2.6). Any help or hint is appreciated,  
thanks in advance.

Best regards,
Peter





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