VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 10 2005 - 10:52:00 CDT

Hi,
  Do these two structures have the same general topology, none of them
are reversed/flipped or have some other symmetry right? One thing
that will help elucidate what's going on would be to use the same
selection and draw a VDW rep so that you can see what the relationship
between the aligned structures is, and whether one of the atoms you're
selecting is preventing good alignment for some reason.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 06, 2005 at 03:37:24PM +0200, Peter Schellenberg wrote:
> Hi,
>
> I asked this before, but did not get an answer, I hope it is ok to
> try again: If I overlap two protein structures in VMD by selecting a
> large part of the backbone according to the description in the VMD
> Molecular Graphics Tutorial, chap. 2.5, everything works fine.
> However if I try to overlap two almost identical digoxin- type
> steroids bound to proteins and just select the corresponding steroid
> atoms, it does not give the wanted result:
>
> set antibody [atomselect 3 "all"]
>
> set steroid_dtx [atomselect 1 "type O14 O21 O23 C5 C6 C12 "]
>
> set steroid_dgx [atomselect 3 "type O14 O21 O23 C5 C6 C12"]
>
> set M [measure fit $steroid_dgx $steroid_dtx]
>
> $antibody move $M
>
> ( O14, O21 etc refer to the same chemical position in both steroids).
> The steroids overlapp along their long axis, but perpendicular to
> each other, but in the way that O14, O21 are not close to each
> other, but rather at opposite ends. The same happens if I use the
> index selection. Is there any solution to this problem?
>
> Kind regards Peter
>
>
> Dr. Peter Schellenberg
> Institute for Physical High Technology Jena
> Dept. of Biotechnical Microsystems
> Albert -Einstein -Str. 9
> D-07745 Jena
> +49 -3641 -206 308 

-- 
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