You're probably already aware of it, but the the Ramachandran Plot Explorer does the first two things on your list. I tried to use it in a large lecture, but it wasn't as effective as I'd hoped. However, it is quite useful in smaller group settings. I believe it is open source and you may even be able to get the person who wrote it to add feature 3. It would be much more effective if it showed the van der Waal's collisions, but I've gotten busy and haven't pursued it. You can download the Ramachandran Plot Explorer from http://www.dillgroup.ucsf.edu/~bosco/rama.html. If you come up with anything better, I'd be interested. Jon ****************************************** Jon R. Stoltzfus, Ph.D. Michigan State University Biochemistry and Molecular Biology Office: 305 Biochemistry e-mail: stoltzfu at msu.edu Phone: 517 432-8775 -----Original Message----- From: molvis-list-bounces+stoltzfu=msu.edu at bioinformatics.org [mailto:molvis-list-bounces+stoltzfu=msu.edu at bioinformatics.org] On Behalf Of Eric Martz Sent: Wednesday, June 07, 2006 11:05 AM To: molvis-list at bioinformatics.org Subject: [Molvis-list] Interactive visualization of phi/psi? [Apologies if you already received this via pdb-l] I have been looking for interactive visualizations of phi/psi to help convey the steric basis for the Ramachandran plot. Ideally, I would like: 1. Model freely rotatable with the mouse, to view from any perspective, 2. Phi and psi angles freely and independently rotatable, 3. Unequivocal visual indication of van der Waals collisions, such as those great red baskets in KiNG. These two below are much less important than 1-3 above. 4. Visualization in browser rather than stand-alone application. 5. Works on OSX and linux as well as Windows. Please let me know of resources with any of these capabilities. The closest I have found is the kinemage 2literacy.kin by Simon Lovell at http://www.bioinf.man.ac.uk/~lovell/kins.shtml This has 1 and 2 above, but neither 3 nor 4. Is there some way to turn on the red collision baskets in this kinemage? Could it be shown in KiNG, or would that sacrifice the slider controls? Other useful resources I've found are - An animated gif at http://speedy.st-and.ac.uk/~naismith/teaching/lectures/3014/lecture/Rama_ani mationhtm.htm that shows separate, side by side "canned" rotations, by J.H. Naismith. Meets none of 1-4 above, but does convey the general idea clearly and quickly. - A rather nice quicktime movie from Univ. Wisc. La Crosse http://visu.uwlax.edu/BioChem/Rotate.mov This partially meets #1 above (via the quicktime slider) but the non-standard element colors make it very confusing. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ _______________________________________________ Molvis-list mailing list Molvis-list at bioinformatics.org https://bioinformatics.org/mailman/listinfo/molvis-list