From: Axel Kohlmeyer (
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 ).

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


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

Axel Kohlmeyer
   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.