Dear Angel, Bob, and others concerned with the definition of carbohydrate in Jmol:
Apparently Jmol defines 'carbohydrate' as a list of carbohydrate residues that occur in the PDB: http://wiki.jmol.org/index.php/AtomSets/Carbohydrate Earlier I constructed my own such list for use within FirstGlance, but since the Jmol 12 list given in the above-cited page is longer, I have retired my list and I will trust Jmol to know what 'carbohydrate' is. A single PDB entry, 1rpj, includes allopyranose/allose, with the ID [ALL]. When last I tried using this, it caused my scripts to die. I notice that it is not included in the list given in the wiki page cited above. Presumably it should be included. I notice that [ALL] now selects it, but 'carbohydrate' does not. Probably the Jmol defininition list needs to be updated in general, but 1rpj was deposited and released in 1999. Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org FirstGlance, used by Nature - http://firstglance.jmol.org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Interactive Molecules in Public Spaces http://MolecularPlayground.Org Workshops: http://workshops.molviz.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
