Animations of protein conformational changes are one of the most impressive and informative modes of molecular visualization (http://morphs.proteinexplorer.org ). Unfortunately, I think Jmol applet's maximum speed of animation (frame display rate) is too slow to convey motion effectively except for smaller proteins with few total frames. This situation is dissuading me from implementing animations of the latest structural discoveries, and animation authoring tools for Jmol in Protein Explorer.
There are two problems for which I am advocating improvements in the Jmol applet. 1. First, when the frames per second (fps) requested of Jmol is more than it can achieve (with "anim mode palindrome 0.01 0.01"), it skips frames. We need a setting to insist that Jmol show all frames, even when it cannot achieve the requested fps. 2. Second, the maximum fps of which Jmol is capable is too slow. It is several fold slower than the maximum of which Chime is capable, and that was already a bit too slow for larger proteins with sets of 15-20 frames. On current Windows XP SP2 computers (3 gigaHerz, with 512 megabytes of RAM or more), Chime needs only 43-64 milliseconds/frame for my test data (see below), and it does not skip frames. In contrast, the fastest frame rate Jmol 11.1.15 using Java 1.5.0_11 can achieve is about 215 milliseconds, or 3.4 to 4.9 fold SLOWER. On a current Intel Mac OSX 10.4.8 (about 2 gigaHerz core 2 duo, 1 gigabyte RAM, java 1.5.0_07) Jmol's fastest animation rate is about 140 milliseconds/frame. (I have no test data here for Chime yet. Note that on such a computer, Chime will probably need less than 43 mS/frame.) TEST WEBSITE http://www.umass.edu/microbio/chime/beta/jmol/animrate Here I have the same animation in Chime and Jmol. The Jmol can be run at fps 2, 4, 6, 8, or 12. The shortest time per frame is typically achieved at 8 or 12 fps (but frames may be skipped). I stopwatched ten cycles. There are 14 frame changes per cycle, so 140 in 10 cycles if no frames are skipped. The fastest speed Chime can achieve is with little or no delay between frames. This occurs with the first link after "Chime", labeled "Delay 0.01 NO DOTS". The test animation displays with acceptable speed in Jmol, but this is because it contains only eight models (eight frames). A smoother animation with 12-16 frames would be better. Further, the test animation model is relatively small, 2,962 atoms/model (times eight models, total file size 1.6 megabytes uncompressed). For example, a morph between two states of the calcium transporter would have about 8,000 atoms/frame. The total filesize of a 16-frame morph would be about 10 megabytes uncompressed. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
