VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Mar 07 2008 - 10:23:46 CST

On Fri, 7 Mar 2008, Ignacio Fernández Galván wrote:

IFG> Hi all,
IFG>
IFG> Is it possible to control the RMSD Trayectory Tool plugin from a
IFG> script, with text commands?

not as such. you could look through the code and see whether
you can reuse the available procs for your script.

IFG> Also, I had two molecules, each of them with associated volume data. I
IFG> aligned both molecules with the RMSD plugin, but the volume data stayed
IFG> in the old position and orientation. Is it possible to move the volume
IFG> data as well?

no. at least not directly. you could record the transformation
matrix and apply it to the grid base vectors manually, but you'd
have to do that manually and it would only work with some file
formats, as several molfile plugins rotate coordinates and
associated data to have the coordinates and the volumetric
data arranged in a way so that periodic display is correct.

cheers,
   axel.

IFG>
IFG> Thanks,
IFG> Ignacio
IFG>
IFG>
IFG> ___________________________________________________________
IFG> Rise to the challenge for Sport Relief with Yahoo! For Good
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IFG> 

-- 
=======================================================================
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.