VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Mon Nov 28 2005 - 14:56:54 CST

On Sun, 27 Nov 2005, ed mendez wrote:

EM> Dear guru.

dear ed,

EM> I need to update the colors in a VMD movie.
EM> I know how to select atom types, but these are not
EM> recomputed on each frame! (even by selecting the
EM> option
EM> in "Graphcal Representation/trayectory/update
EM> selection ..."
EM> I have gone crazy changing all king of parameters.
EM>
EM> I also tried scripting ...

well, you can try one of the strategies suggested at:
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect4

or something similar, by e.g. first reading the coordinates and ignoring
the fact, that the atom types change and then in a second step re-read
the file from a script and store the atom type in the user field.

now you could create a number of visualizations with selections of the
type 'user = xxx' for each atom type and also a dynamics bonds selection
with the color set to grey and then pat yourself on the back ;-).

EM> (each frame should get recomputed atom types).
EM> If this is not possible, how can I read these from
EM> different files, and then
EM> visualize in a simulation one at a time?.

EM> I would like to do this for files containing hundreds
EM> of atoms, and hundreds of frames,
EM> so doing this manually is not an option :(

have a look at.
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect5

feel free to ask, if you have any additional questions.

regards,
    axel.

EM>
EM> Your help would be appreciated.
EM>
EM>
EM> Eduardo Mendez
EM> The Sailor from the Prairies
EM> U of S. Chemistry
EM>
EM>
EM>
EM>
EM>
EM> __________________________________
EM> Yahoo! Mail - PC Magazine Editors' Choice 2005
EM> http://mail.yahoo.com
EM> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.