VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Oct 21 2008 - 09:01:22 CDT

On Tue, 21 Oct 2008, Tomek Wlodarski wrote:

TW> Dear vmd users,

dear tomek,

TW> I am generating density map (for all atoms) for one structure with 0.5
TW> A grid size, atom size radius 1x and without weights.
TW> Then I would like to fit to this density map another structure, of
TW> course If this is the same protein, but in different conformation I
TW> could superimpose it, but I am searching more elegant way of doing
TW> this :)

what about a regular rmsd fit? since you don't compute a real
electronic structure, the atom centers should be as good to
fit to as the resulting superposition of spherical densities.

TW> Also it would be good to get some numbers - as a measure of how this
TW> other structure fits to density map.
TW> It is possible in VMD to fit structure to this volumetric data?
TW> I was thinking about some crystallographic software which are fitting
TW> structure to electron density map, but I do not know if this software
TW> could do the same with .dx files (as electron density map)...
TW> Do you know way of fitting rigid structure to density map generated in
TW> VMD (in dx format) or to convert dx file for this purpose?

the dx format generated by VMD is a simple 3d grid and almost
self-documenting (otherwise you can look up all details of the
dx format somewhere under http://www.opendx.org/ ).

to the best of my knowledge, VMD does not have any tools like that
integrated, feel free to write one.

cheers,
   axel.

TW> Thanks for any advice :)
TW> Best
TW>
TW> Tomek
TW> 

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