VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 29 2007 - 11:31:05 CDT

Hi,
  As you've already noticed, the current implementation of the Mouse->Move
feature doesn't affect volumetric maps loaded into a molecule. I agree
that Mouse->Move->Molecule should be changed to affect the contained
volume data as well. I'll add this to the TODO list and let you know
when I have something for you. In the mean time, a cheap sleazy way of
getting what you want is to toggle the other molecules "fixed" (double
clicking the "F" in the molecule status line in the main VMD menu)
and then translate/orient the molecule as you see fit. This will not
change the atom coordinates or map coordinates however, so it isn't a
complete solution if you want to edit the map and save it back out.

We are planning to make a large number of improvements to the manipulation
of volumetric datasets in VMD, subsequent to 1.8.6. Between GPU acceleration
of some of the computationally demanding map processing routines and
various representation, GUI, and scripting updates, I expect that these
updates will be quite an improvement over what we have presently,
and will address most of the things people have been asking for recently.

Cheers,
  John

On Thu, Mar 29, 2007 at 05:05:40PM +0200, Avell Diroll wrote:
> Dear VMD-L,
>
> I would like to place a protein inside a membrane. For that purpose I am
> using VMD move tool (mouse->move->molecule) to superpose the membrane
> and the protein.
> In order to adjust the protein placement/orientation I load the protein
> lipophilicity potential map and displays it as isosurfaces. I would like
> to move the protein with its map but the VMD move tool leave the volume
> data in place.
> Is there a way to move the volume data (or a fixed representation of the
> data) with the protein?
>
> Thanks for any help
>
> Regards,
>
> Julien
>
> PS: for those interested, I just posted the code to generate the
> lipophilicity potential maps, you may find it here:
> http://code.google.com/p/pymlp/
>
>
>
> --
> __________________________________________________________________________
> Julien Lefeuvre - PhD student
> Institut Européen de Chimie et de Biologie (IECB)
> UMR 5248 CBMN «Chimie et Biologie des Membranes et des Nanoobjets»
> CNRS-Universite Bordeaux 1-ENITAB
> 2, rue Robert Escarpit - 33607 Pessac Cedex - France
> Tél. : 33 (0)5 40 00 30 31
> Fax. : 33 (0)5 40 00 30 73
> http://www.iecb.u-bordeaux.fr
> __________________________________________________________________________ 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078