All, Although I am a big fan of using computer visualization in the classroom and lab for macromolecules, I really think that this is one case where using models the students can hold in their hands is preferable. I require them to bring a prebuilt peptide to class when we discuss phi/psi angles and they can also use it on the exam. Nothing beats having the atoms actually crash into each other to give students the idea of what steric conflict means. Once they have that obvious example down (like phi=0,psi=0), we can discuss the idea of atoms having an electron cloud and the areas of the Ramachandran plot with conformations that are energetically unfavorable, but not as bad as 0,0. We use the Darling models (http://www.darlingmodels.com/ccp51/cgi- bin/cp-app.cgi) and I bring tape to class so that they can fix the trans orientation of the peptide bond. Darling also makes a special peptide bond model (http://www.darlingmodels.com/ccp51/cgi-bin/cp- app.cgi? usr=51F562948&rnd=198151&rrc=N&affl=&cip=149.106.224.2&act=&aff=&pg=prod &ref=kit_15b&cat=kit_specialized&catstr=HOME:kit_specialized) that can be used and is only $2. Our students use these models in organic chemistry so they already have the kits. Kristin On Jun 7, 2006, at 11:05 AM, Eric Martz wrote: > [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_animationhtm.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 Kristin Fox Associate Professor of Chemistry Director of Biochemistry Union College 807 Union Street Schenectady, NY 12308 Phone: (518) 388-6250 Fax: (518) 388-6796 foxk at union.edu