From: Axel Kohlmeyer (
Date: Thu Mar 20 2008 - 05:37:31 CDT

On Thu, 20 Mar 2008, SENTHIL KUMAR wrote:

SK> hi , i wish ti calculate rmsd for some 30 similar RNA structures from
SK> various pdb sources.
SK> an earlier program did not pik up hetatm and i realised it late :(
SK> can you let me know how to do it in vmd , i knew the plugins in vmd.
SK> but how to do in commnad line tcl console and how to feed all the

please see the user's guide and related tutorial on how
to do scripting in vmd.

you load molecules with 'mol new', build proper selections
and then call 'measure rmsd'. the plugins are just front
ends for that. it may be useful to have a look at the
plugin script code to gather a few additional ideas on
how to get it done in a clean way.


SK> files so i can run all with all rmsd calculation

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.