I am using sync in my Jmol Tutorial-Authoring Template (JTAT) when multiple molecules are displayed side by side. I send "sync * on" to only one Jmol, the last one. I think sync is very important, but there is one major inadequacy in the present implementation.
The problem arises when comparing two different molecules. When the molecules being synched are not aligned in their coordinate systems (as is typically the case for independent crystallographic results), sync is not working satisfactorily. An example is View 5 in Chapter 3 at the JTAT Demo (http://bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_comp/chapter.htm ) With Chime, you to move one molecule relative to the other (with synch off). Then, when you turn on synch, the relative orientation is maintained. Also each molecule rotates about its own center of mass, but in synch with the other(s). I think this is what is needed in Jmol. Perhaps a new Jmol command is needed to record the relative orientations, and maintain those in the sync'ed state? Also some mechanism is needed to rotate each molecule about its center of mass by default, rather than the other molecule's center of mass. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
