VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Wed Aug 17 2005 - 11:31:15 CDT

Dear vmd users,
   I am trying to perform an overlay of more than 2 molecules using the
script below. It happens that the second molecule is not moved on top of
mol. 0 (molecule 1 is moved properly). I guess is something about the
order of selecting the molecules. Could somebody correct my script so
that the molecule 2 will also be moved on top of molecule 0?
   Also I would like to continue this overlaying until up to 6
moilecules. Is there any trick that I shall take care of?
Thank you very much.
Best wishes
vlad

logfile vmd.log

mol load pdb RRM-model_o.pdb
mol load pdb 1aud.pdb
mol load pdb 1dz5.pdb

set sel0 [atomselect 0 {{name C CA N O} and {resid 6 to 8 32 to 35 46 to
50 76 to 78}}]
set sel1 [atomselect 1 {{name C CA N O} and {resid 10 to 12 40 to 43 54
to 58 83 to 85}}]
set sel2 [atomselect 2 {{name C CA N O} and {resid 10 to 12 40 to 43 53
to 57 83 to 85}}]

set tm1 [measure fit $sel1 $sel0]
set tm2 [measure fit $sel2 $sel0]

set move_sel1 [atomselect 1 all]
set move_sel2 {atomselect 2 all]

$move_sel1 move $tm1
$move_sel2 move $tm2

measure rmsd $sel1 $sel0
measure rmsd $sel2 $sel0 

-- 
Vlad Cojocaru                                  
Max Planck Institute for Biophysical Chemistry  
Department of Molecular Biology                
Am Fassberg 11, 37077 Goettingen, Germany      
tel: ++49-551-201.1327                         
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de