At 3/17/08, Bob Hanson wrote: >I'm ready to tackle two big Jmol feature requests: > >1) automatic conversion 2D to 3D >2) minimal molecular mechanics support
I'd like to bring up a third possible big addition: built-in sequence-to-structure mapping. I an envisioning this as an optional separate applet display rectangle that would show a macromolecular sequence listing. Touching a (one-letter code) residue would display its 3-letter code and maybe full name, and its sequence number. Clicking on a residue, or block-selecting a range of residues would highlight them in the 3D rendering in a manner that could be configured. Clicking a residue in the 3D rendering would highlight it in the sequence listing. Optionally, the residues in the sequence listing could be colored the same as in the 3D display. This could equally well be implemented outside of Jmol as I have done (outside of Chime) in Protein Explorer's Seq3D interface. But if it were built into Jmol (as a separate optional module) then it would always be available in all Jmol pages -- which I see as a huge advantage. Two years ago, I wrote specifications for such a sequence-to-structure interface: http://molvis.sdsc.edu/fgij/seqspecs.htm (there are also example problematic PDB files there) I did this because the implementation in Protein Explorer has some serious inadequacies. I would be thrilled if a volunteer would develop the needed interface, either within Jmol or outside it. I have no plans to do it myself because I have too many other irons in the fire. Of course I'd be very willing to help test it. -Eric ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
