>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. At 2/14/06, Gale Rhodes wrote: >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? You are correct. Stereo is backwards. I noticed this myself about a week ago and reported it to jmol-users, so it will be fixed. >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. Good idea. I'll add it. > 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.) I do not find this to be true for ensembles of NMR models, e.g. 2BBN. However, it may be generally true for minimized average models, e.g. 2BBM -- but these are often not published in the PDB. Perhaps you are "thinking DeepView", which may have such a color scheme calculation built-in? > 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. I agree these are very important, but I'm not convinced they should be built into Jmol. Rather, I'll add a link (under "More Views..") to the Richardson's outstanding MolProbity (http://kinemage.biochem.duke.edu/molprobity/index-king.html), which nicely handles all of these issues in a java-based viewer (KiNG). >3) Finally, thanks to Jmol developers for giving what looks like a >solid foundation for many powerful tools for molecular viewing and >analysis. Hear hear! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */