VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Thu Jul 10 2003 - 07:13:07 CDT

Dear VMD users,
   I am trying to do the following:
  I have an RNA molecule (from a crystal structure) which containd 2
helices and 1 loop. I am trying to extend the helices with 7-10 base
pairs. So I created the A-RNA helices by including a GC base pair common
to the crystal structure..then I was trying to fit the common base pair
(by fitting the base atoms) but the problem is that the fit gave a
strange matrix one of the molecule moves in a very strange position.
Doing it by hand I can see that the common base pair (in tha crystal and
in the extended helix) can be overlayed without any problem. Now I have
a question....Is there another way to overlay common parts of two
molecules in VMD? When selecting the atoms for fit is VMD respecting the
order that I gave to atomselect comand...for instance if I say:
atomselect 0 [{(index 20 14 15}]
atomselect 1 [{index 16 13 19}]
is VMD trying to fit atom 20 (mol 0) to atom 16 (mol 1); atom 14 (mol 0)
to atom 13 (mol 1)...........or does it do it in another way??
Thanks a lot for any advices,
Best regards,
Vlad 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204