In his announcement of 10.9.76, Bob asked for suggestions regarding the dynamic popup menu.
I would like to reiterate an old request. In Chime, the menu Select, Residue lists all 20 amino acids, but grays out any not present in the currently loaded PDB file. Thus, in 1D66, GLY, MET, and PHE are grayed out. This makes it very easy to spot which amino acids are not present. It is a very useful feature of Chime. At the end of the 20 amino acids are listed any other residues (group names) that occur in the model. However, Chime has the bug that nucleotides are not listed! 1. My suggestion is that missing residues be listed (as they are now) but grayed-out in Jmol's Select, Protein, By Residue Name list. 2. Also, nucleotides absent should be grayed out in Select, Nucleic. 3. There is a typographic error in Select, Nucleic: RNA is listed as ARN (in 10.9.70). 4. Since Jmol deems some non-standard (HETERO) residues to be protein, these should be listed in Select, Protein, By Residue Name. I recommend that non-standard residues be listed AFTER the 20 standard amino acids, and separated from that list by a blank line. Thus in 1BKX, SEP and TPO would be on the list. Similarly for non-standard nucleotides (tho I don't recall how Jmol handles these). 1EVV has many non-standard nucleotides. 5. Jmol's Select, Hetero, by HETATM menu is unpopulated (in 10.9.70). 6. I tried to get 10.9.76 but can't find it. Sourceforge lists only 10.9.75, nor did I spot it at Bob's server. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
