VMD-L Mailing List

From: Tomek Wlodarski (tomek.wlodarski_at_gmail.com)
Date: Wed Oct 22 2008 - 04:56:03 CDT

Dear Axel,
thanks for reply!
You are right that averaging structures should give the same result
like averaging density map.
But I wanted not to average density maps- only add them, and after
that try to fit rigid structure.
So for example for all observed rotamers I would not get average
density of rotamers (which would be some kind of fuzzy cloud) but
density map representing all rotamers (calculate density map for each
rotamer, after superimposing, and add this maps). Then to this density
map representing all conformation I would like to try fit rigid
structure.
Best,

tomek

On Tue, Oct 21, 2008 at 10:53 PM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Tue, 21 Oct 2008, Tomek Wlodarski wrote:
>
> TW> Dear Axel,
> TW>
> TW> Frankly I do not know yet how this averaging works, but do you think
> TW> this approach is physical? I mean after averaging do I get structure
>
> in my opinion, it is as physical as averaging over the density maps
> that you create with volmaptool. all you do is replacing the coordinates
> with a spherical density gaussian that has always the same shape (if
> you'd do an electron structure calculation, that would be different)
> for each atom at each step. the result that you get should be equivalent
> of computing a density map for the average structure that is smoothened
> by something that is proportional to the RSMD of the fit for the
> individual atoms.
>
> TW> which could be present in distribution of conformations for this
> TW> protein?
>
> very likely not. but the averaging over density maps has the same
> problem. consider a simple example: a methyl group stuck on a molecule
> that is otherwise fixed in space. if the methyl group rotates freely,
> the the C-H bonds in the averaged structure will collapse. if you
> compute the density map the H atom density will end up as smooth
> density "ring" around the C, you cannot fit a CH3 group into this
> so well (since the density is much lower) and particularly you
> cannot identify the orientation. so basically you end up with
> the same information. the RMSD tells you how much each structure
> will fit to the average and the RMSF tells you how reliable the
> average for each atom is. you can try to improve the fit by picking
> some atom property (mass or other) as weighting parameter.
>
> the RMSD fit will fail, when you want to compare two very different
> structures that have a similar shape. this is where you'd need
> a density (i.e. shape) based approach.
>
> cheers,
> axel.
>
> TW> Thanks for replay,
> 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.
>