VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Oct 07 2005 - 11:20:25 CDT

Dear Peter,
out of curiosity, if for the last step you do $steroid_dgx move $M, does
it align the steroid properly? How far out of place are they initially?
Peter

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
>
>