I am trying to convert some Chime animations to Jmol. These are multiple model NMR-format PDB files.
My test system is Firefox 2 on Windows XP SP2, 768 Megs of RAM, Pentium 4 running at 1.6 GHz. I am using Jmol 11.1.46 applet (just one jar file, JmolApplet.jar). I am impressed with the speed of Jmol's animations -- it seems much improved! QUESTION 1: PAUSE AND RESUME FROM SAME FRAME? I have two buttons that do "anim on" and "anim off". The problem is that although "anim off" freezes the animation at its current position (or close to it), "anim on" starts over from frame 1. One wants to stop the animation at a specific point, then resume it from that point. What are the best commands to achieve this? I tried "save state A; anim off;" then "restore state A". This does resume animation from where it was stopped, but "save state A; anim off;" stops the animation immediately for a few seconds, then jumps one or two more frames. And "restore state A" takes about 5 seconds to work. QUESTION 2: SKIPPING FRAMES. When I run the Chime animation concurrently with the Jmol animation (in the same or different browsers), Jmol's animation skips frames. I interpret this to mean that when the CPU is heavily loaded, Jmol skips frames. Perhaps frames would also be skipped on a slower CPU? Is there any way to prevent skipping frames? Bob: on 3/21/07 you said "Eric, I've added a "forced refresh" each frame so that Jmol does not skip frames." I interpret that to mean I don't have to do any settings to "force refresh" -- I think you mean it is on all the time. Correct? QUESTION 3: OUT OF MEMORY? For awhile I was having trouble getting Jmol to display a 16-model, 10 megabyte PDB file. Deleting half of the file (8 models, leaving 5 megabytes) worked. After I closed a few memory-hog applications that were running concurrently, Jmol was able to display the full 10 meg file. When it failed, Jmol simply left a blank space. Would it be possible to have Jmol somehow report that it (or java) ran out of memory, rather than leaving the user to wait and wonder indefinitely? 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
