Dear Angel, Your points seem valid, and I agree that the workaround is easy enough. Thanks for the detailed consideration! -Eric
At 3/22/08, Angel Herráez wrote: >Eric, I can see what you mean; I've had this >problem before with other PDB files (1GC1). >The problem is in the numbering; the >carbohydrate residues are numbered 901, 902, >clustered at the end of the amino acids. >I agree this is undesired, but can't see how >Jmol can be blamed for it, or imagine how to fix >it. The same could happen if the amino acid >residues in the file were numbered not >following their position in space. > >As a general discussion on Jmol schematic renderings for carbohydrates: > >As far as I know, Jmol understands several >carbohydrate residue names and can draw trace >(and, so it seems, ribbons) between them. I've >used this before to my advantage in drawing >a spiral trace for amylose, for example. > >I dont' think that the capability to recognize >carbohydrate chains as so, and draw for them >some kind of schematic rendering -as for >proteins and nucleics- is a bad thing, and certainly >not a bug. It's true that carbohydrate >recognition is still limited, and their schematic >rendering is so too; I seem to recall that Bob >mentioned the inability to render cartoons is >related to the lack of a reference atom set upon >which to base the direction of the ribbon. > >Anyway, for your problem the fix would be to >restrict selection to protein before using >"ribbons", right? > >Regards, > > > >------------------------------------------------------------------------- >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 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- 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
