VMD-L Mailing List

From: Tomek Wlodarski (tomek.wlodarski_at_gmail.com)
Date: Tue Oct 21 2008 - 15:30:46 CDT

Dear Axel,

Frankly I do not know yet how this averaging works, but do you think
this approach is physical? I mean after averaging do I get structure
which could be present in distribution of conformations for this
protein?
Thanks for replay,
Best

Tomek

On Tue, Oct 21, 2008 at 9:53 PM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Tue, 21 Oct 2008, Tomek Wlodarski wrote:
>
> TW> Dear Axel and Leo!
> TW>
> 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).
>
> tomek,
>
> in that case you'd simply do a fit to an averaged structure.
> you could use the RMSD trajectory tool GUI for that.
>
> cheers,
> axel.
>
> 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>
> TW> Tomek
> TW>
> TW> On Tue, Oct 21, 2008 at 4:14 PM, Leonardo Trabuco <ltrabuco_at_gmail.com> 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> > http://situs.biomachina.org/
> 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> > <tomek.wlodarski_at_gmail.com> 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> >
> 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.
>