VMD-L Mailing List

From: Peter Schellenberg (peter.schellenberg_at_ipht-jena.de)
Date: Thu Oct 06 2005 - 08:37:24 CDT

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