[Molvis-list] Docking in Rasmol?

Herbert J. Bernstein yaya at bernstein-plus-sons.com
Fri Apr 14 22:58:26 EDT 2006

Adding a command to undo the initial centering at any time is feasible.
That is just what is done to write out the original coordinates when
writing a PDB file from RasMol.  Naturally, to preserve the alignment
among molecules that have been docked the coordinates of all but
one molecule would have to be modified.   Here are the commands
I would propose to add:

1.  recenter off -- would turn off recentering for all current and subsequent
                 loads of molecules

2.  recenter on --  would restore the recentering of all current and
                 subsequent loads of molecules

3.  write modified <type> <filename> -- would write out the current
                 molecule with the coordinates modified to incorporate
                 the changes made to create the display

The resulting set of files could then be reloaded into RasMol or any
other program accepting multiple molecules to recreate the docked
configuration. You would have to put in a recenter off command.  I
don't want to disable existing scripts by making recent off the
default, but it is easy to set up an initialization script for
RasMol, to effectively make this the default behavior.  Making RasMol
do the merge of multiple datasets internally on to one will take
a little longer, and will probably need to be to WPDB or mmCIF format


At 11:24 AM -0700 4/14/06, Kevin Karplus wrote:
>I would favor having rasmol do as little to the coordinates as
>possible---turn off the recentering by default, since it only takes
>one command to recenter, but there is no way to recover from recentering.
>Being able to hand-dock ligands and multimers would be a great
>advantage in protein structure prediction and protein design.
>Loading the ligands from separate files then outputing the complex as
>a single file would be very useful.
>Kevin Karplus	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
>Professor of Biomolecular Engineering, University of California, Santa Cruz
>Undergraduate and Graduate Director, Bioinformatics
>(Senior member, IEEE)	(Board of Directors & Chair of Education 
>Committee, ISCB)
>life member (LAB, Adventure Cycling, American Youth Hostels)
>Effective Cycling Instructor #218-ck (lapsed)
>Affiliations for identification only.
>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
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                  yaya at dowling.edu

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