[MMTK] about visualization

Konrad Hinsen research at khinsen.fastmail.net
Mon Dec 17 15:11:47 UTC 2012

子茗 writes:

 > what I want to do is to draw a picture of the protein under a certain mode,and the
 > protein is scaled by diffirent color according to the vibration of the part,say red
 > represents vibrate violently, and blue represent soft,  so how can I do it ?

It can be done, but it is unfortunately a bit complicated. The trick
is to create a PDB file in which the quantity you want to show (in
your case each atom's displacement amplitude in a normal mode vector)
is encoded as a B factor, using a scale from 0 to 99. You can then
tell VMD to use a color scale as a function of the B factor.

I have done this many years ago, but I can't find the Python script
any more. Perhaps someone else has a script that can serve as a
starting point. The basic trick is to assign a value to the attribute
"temperature_factor" of each atom object. That value will then become
the B factor when a PDB file is written.

I wish there were a better way to do such visualizations, but
unfortunately the common visualization programs take all their input
from a PDB file, so everything has to be in there.

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

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