From: Tomek Wlodarski (
Date: Tue Oct 21 2008 - 14:46:15 CDT

Dear Axel and Leo!

Thank you very much for your fast replay!
Axel: I have decided not to use normal RMSD fit because I wanted to
fit to one map representing couple of conformations (after adding
maps for each conformation).
Thanks Leo for this link for sure I will try this Situs program, and
when I found this program adequate to my problem I will ask you for
your script- Thanks!
I have the same sequence :)


On Tue, Oct 21, 2008 at 4:14 PM, Leonardo Trabuco <> wrote:
> Czesc Tomek,
> To rigid-body dock atomic structures into density maps, I would
> recomend you take a look at the Situs program:
> I have code to convert dx maps into situs format; it's not ready for
> release, but I can share it with you in case you're interested.
> If your goal is to simply superimpose structures which don't contain
> the same sequence, I suggest you try the STAMP structure alignment
> tool available in the VMD plugin Multiseq.
> Cheers,
> Leo
> On Tue, Oct 21, 2008 at 7:55 AM, Tomek Wlodarski
> <> wrote:
>> Dear vmd users,
>> I am generating density map (for all atoms) for one structure with 0.5
>> A grid size, atom size radius 1x and without weights.
>> Then I would like to fit to this density map another structure, of
>> course If this is the same protein, but in different conformation I
>> could superimpose it, but I am searching more elegant way of doing
>> this :)
>> Also it would be good to get some numbers - as a measure of how this
>> other structure fits to density map.
>> It is possible in VMD to fit structure to this volumetric data?
>> I was thinking about some crystallographic software which are fitting
>> structure to electron density map, but I do not know if this software
>> could do the same with .dx files (as electron density map)...
>> Do you know way of fitting rigid structure to density map generated in
>> VMD (in dx format) or to convert dx file for this purpose?
>> Thanks for any advice :)
>> Best
>> Tomek
> --
> Leonardo Trabuco, Ph.D. candidate
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign