[MMTK] Visualization

Konrad Hinsen research at khinsen.fastmail.net
Thu Nov 3 08:24:09 UTC 2011

On 3 nov. 11, at 07:21, James Starlight wrote:

> Warning: No viewer with animation feature defined.
> How I can specify to use VMD for animation?

Set up the environment variable PDBVIEWER to point to vmd, i.e.

	export PDBVIEWER=/path/to/vmd

for bash or

	setenv PDBVIEWER /path/to/vmd

for csh.

If the name of the script (the last part of the full path) is "vmd",  
MMTK knows it's vmd and activates animation features. If your setup  
allows to call VMD for static structures but not for animation, then  
most probably your executable is not called "vmd".

For Mac users, this takes one more step because VMD on the Mac does  
not come with a command line script. You have to create your own,  
which looks like the following:

--- vmd --------------------------------------------
xterm -e '/Applications/VMD 1.8.7.app/Contents/Resources/VMD.app/ 
Contents/MacOS/VMD' $*

You need to adapt the path to your VMD installation of course.

> Also I wounder to know if I can save my modes in trr, trp or other  
> trajectory formats supported by VMD?

The standard way to visualize modes is the one you already used:

> from MMTK.Visualization import view
> view(modes[6], 15.)

This creates a four-step trajectory in the form of four PDB files and  
feeds it to VMD in loop mode.

If you prefer to create a trajectory file, there are two choices:

1) use MMTK's native netCDF format, which VMD can read
2) use DCD (the CHARMM and NAMD format), together with a compatible  
PDB file

The "Trajectories" folder in the example script directory provides  
starting points for both approaches.

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