From: Axel Kohlmeyer (
Date: Tue Oct 21 2008 - 14:53:57 CDT

On Tue, 21 Oct 2008, Tomek Wlodarski wrote:

TW> Dear Axel and Leo!
TW> Thank you very much for your fast replay!
TW> Axel: I have decided not to use normal RMSD fit because I wanted to
TW> fit to one map representing couple of conformations (after adding
TW> maps for each conformation).


in that case you'd simply do a fit to an averaged structure.
you could use the RMSD trajectory tool GUI for that.


TW> Thanks Leo for this link for sure I will try this Situs program, and
TW> when I found this program adequate to my problem I will ask you for
TW> your script- Thanks!
TW> I have the same sequence :)
TW> Best!
TW> Tomek
TW> On Tue, Oct 21, 2008 at 4:14 PM, Leonardo Trabuco <> wrote:
TW> > Czesc Tomek,
TW> >
TW> > To rigid-body dock atomic structures into density maps, I would
TW> > recomend you take a look at the Situs program:
TW> >
TW> >
TW> >
TW> > I have code to convert dx maps into situs format; it's not ready for
TW> > release, but I can share it with you in case you're interested.
TW> >
TW> > If your goal is to simply superimpose structures which don't contain
TW> > the same sequence, I suggest you try the STAMP structure alignment
TW> > tool available in the VMD plugin Multiseq.
TW> >
TW> > Cheers,
TW> > Leo
TW> >
TW> > On Tue, Oct 21, 2008 at 7:55 AM, Tomek Wlodarski
TW> > <> wrote:
TW> >> Dear vmd users,
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 :)
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?
TW> >> Thanks for any advice :)
TW> >> Best
TW> >>
TW> >> Tomek
TW> >>
TW> >>
TW> >
TW> >
TW> >
TW> > --
TW> > Leonardo Trabuco, Ph.D. candidate
TW> > Theoretical and Computational Biophysics Group
TW> > University of Illinois at Urbana-Champaign
TW> >

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.