VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Fri Apr 11 2014 - 07:16:17 CDT

Dear all,

I have a rather simple question but for which I did no figure an answer
yet ... I have 2 DNA molecules which I want to superimpose.
The superposition should be done like this:

res 1 from mol 1 on res 10 from mol 2,
res 2 from mol 1 on res 9 from mol 2,
res 3 from mol 1 on res 8 from mol2,

.. and so on ...

If I do the selections "resid 1 to 3" and "resid 10 to 8", it does not
work as VMD tries to superimpose 1 on 8, 2 on 9, and 3 on 10.
I also tried to change the residue numbers in mol 2 such as res 10
becomes res 100, res 9 becomes res 101, res 8 becomes res 102 (to have
ascending order). However, still no success, VMD does not care about the
residue number, it still tries the same. ...

Do I need to change all atom indices to actually make VMD superimpose
the way I want ? Or is there an easier solution to this ?

Thanks for any advice ..

Best wishes
Vlad 

-- 
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru