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. Comments? -- Herbert J. Bernstein At 12:30 AM -0500 4/14/06, Michael Sternberg wrote: >Hello, > >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 >https://bioinformatics.org/mailman/listinfo/molvis-list -- ===================================================== 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 =====================================================