On Feb 13, 2006, at 1:53 PM, Eric Martz wrote: > A new version of FirstGlance in Jmol (http://firstglance.jmol.org) > has been released. Great job, Eric! A couple of things about Jmol itself: 1) Is it just me, or are Jmol's new (v. 10.00.46) stereographic options backward? I'm referring to [Render:Stereographic:Cross-eyed (or Wall-eyed) viewing.] I believe that the current Jmol has them reversed. I get cross-eye stereo (convergent) when I ask for wall-eye (divergent) and vice versa. If I use the console to turn on stereo, the command "stereo 4" gives wall-eye, just as I expect from RasMol or DeepView. And the console command "stereo -4" gives cross-eye. But the menu commands don't seem to be doing the same thing. Any other stereo users out there want to check? Stereo is only available if the viewer has been upgraded to Jmol 10.00.46. Firstglance and the samples at Jmol home are upgraded. PDB's Jmol viewer and the ProteinGlimpse Widget are not. 2) One can always think of something to add to these wonderful tools. It occurred to me, as I was preparing a talk on judging model quality, that Jmol has no built-in options for helping model users to validate models. a) Color by B-factor should be a simple addition, and B-factors can alert you to certain kinds of model problems. With the same command, NMR models are colored by how much each atom's position varies across the ensemble of models (rmsd from the average position), also a quality indicator. (The same PDB file column that contains B-factors for x-ray models contains rmsds for NMR models, and contains uncertainty indicators for homology models, so one command fits all.) b) A more useful tool in model validation is a Ramachandran diagram, which can expose even some rather subtle model errors, and can be useful in sorting out alternative templates for homology modeling. Modelers avoid templates that have a lot of Ramachandran outliers. The resulting model will have the same outliers. c) Other useful tools would be "Select:Clashing Residues" and "Select:Residues with unsatisfied H-bonds." The latter finds buried polar side chains that are probably in the wrong place. Such errors are present in many PDB files, and occur commonly in routine modeling from sequence data using PDB models as templates. Viewers that do not have model validation options make all models look good, and that's not the truth. 3) Finally, thanks to Jmol developers for giving what looks like a solid foundation for many powerful tools for molecular viewing and analysis. Cheers! Gale Rhodes, Professor of Chemistry University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 http://www.usm.maine.edu/~rhodes