From: Vlad Cojocaru (
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

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]