VMD-L Mailing List

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 12 2006 - 10:18:35 CDT

On Fri, Sep 08, 2006, Nadia Vahdati wrote:
>
> I am trying to view my normal modes calculated in Nmode(amber9). I
> understand that the IED plug-in (VMD-1.8.2) can display the modes, providing
> the vector file is given the .pev extension.
>
> I have used IED before for small molecules to display the modes and had no
> problem, however now I am trying to view the modes of a large protein
> system (4962 atoms). When the Eigenvectors are loaded, I can only see very
> vague movements. I was wondering if there is anything I need to do to the
> files before viewing them in IED apart from changing the vector file
> extension.
>

Look at line 95 of ied.py (I'm using version 2.02):

   self.prjLim = [(-50,50) for v in transpose(self.prj)]

Change "(-50,50)" to something like "(-2000,2000)" for a big molecule.
You may have to play around with the exact number to use.

Extra credit: calculate this value based on the number of atoms, or the
character of the eigenmode, or something like that. Or, add a widget that
allows this value to be modified by the user.

....hope this helps....dave case