[Molvis-list] Docking in Rasmol?

Herbert J. Bernstein yaya at bernstein-plus-sons.com
Fri Apr 14 08:46:42 EDT 2006

The internal data structures support your idea, but there are other
issues to resolve.

Usually the positioning changes done to a molecule in RasMol are
exported in a script, rather than in a coordinate file, because
the program centers molecules on load, so on reloading each
molecule needs to be shifted again.  One way around this would
be to add the option of writing out the ensemble with molecules
wrapped in model - endmodel brackets, which would allow the
position changes to be preserved.  Another solution would be
to add a mode of molecule loading, or a post loading command
that disables the initial recentering, as well as your suggested
revision to the write command, so that molecular repositioning could
be preserved in the coordinate files and not just in scripts.  The
information is there.  We just need to settle on the user externals.


   -- Herbert J. Bernstein

At 12:30 AM -0500 4/14/06, Michael Sternberg wrote:
>I am looking for a program which can read multiple molecules and 
>allows the user to reorient each one and save the combination, i.e., 
>supports a "docking" feature.
>Now, Rasmol-2.7.x does support multiple molecules and can save each 
>one in its present orientation (at least in the alchemy format), but 
>does not track translation.  This is tantalizingly close.
>What's needed is essentially a displacement correction upon "write 
><format> <file>".  Do the current internal data structures support 
>such an extension?
>Regards, Michael
>Michael Sternberg, Ph.D.         | Argonne National Laboratory
>phone: (630) 252-7020 fax: -9555 | Materials Science Div., Building 200
>email: sternberg.at.anl.gov      | 9700 S Cass Ave, Argonne, IL 60439-4831
>Molvis-list mailing list
>Molvis-list at bioinformatics.org

  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

               Office:  +1-631-244-3035
            Lab (KSC 020): +1-631-244-3451
                  yaya at dowling.edu

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