Eric, please submit this as a feature request, and I will take a look at it. My first reaction to the Word document is that I think the Chime rendition looks horrible, but that may be just because they used a poor algorithm. I think we would have to experiment a bit, but I'm willing to try. I've recently streamlined the graphics part of Jmol, so redoing the cartoon business is not out of the question.
Bob > I would like to request that Jmol's rendering of secondary structure > cartoons be improved. In my opinion, its 'cartoon' rendering is very > important but unsatisfactory. With increased exposure (Nature is working > on > installation of FirstGlance in Jmol), the present rendering may diminish > Jmol's acceptance/reputation. > > Presently, Jmol draws beta planks as absolutely straight. In reality, beta > strands are often curved and usually somewhat twisted. > > In some cases, Jmol's beta strand planks not only largely miss the correct > positions, but end up crossing through each other. This happens for 1APM > (restrict 42-75 to see the relevant portion). > > Similarly, many alpha helices are curved, and Jmol's rockets need to > reflect this. > > Also, the cone-heads of Jmol's rockets (very nice) sometimes "flap" > annoyingly when the molecule is rotating. Though less important, it would > be great if this could be fixed. > > I have put an MS Word 2002 file, ss-cartoon.doc, containing snapshots of > some cases where Jmol's rendering is unsatisfactory at: > http://www.umass.edu/microbio/chime/beta/jmol/ > Snapshots there compare the renderings of Jmol, Chime, and Protein > Workshop. > (If anyone has trouble displaying the .doc file, let me know.) > > -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 > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > ------------------------------------------------------------------------- > 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 > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
