I have been trying to develop a script that animates a multiple-model PDB file, forward direction only, in "animation mode once", with some rotation between animation cycles. Testing in Jmol application 11.9.1, the script below crashes Jmol reproducibly after the first cycle of animation and before the second. I've seen similar crashes, but tested less thoroughly, in Jmol application 11.6.14 and 11.8.2.
By "crash", I mean that the second animation never happens, and the molecular image freezes -- you can't rotate it with the mouse. It "never" recovers (20 min or so). While "frozen", you can raise the menu and enter commands but there is no response. For example "select all" reports no atom count, and items on the menu have no effect on the molecular rendering. Tests done in fully up to date Mac OS 10.5.8 with Apple Java 1.5.0_19. I would like my script to work in Proteopedia, which is currently using Jmol applet 11.6.14. Therefore I'm not using the latest greatest syntax, for compatibility with 11.6.14. Eventually Proteopedia will upgrade, but its a bit of work to make sure everything is OK so its not done too often. The 21 model PDB file I'm using is Hivpi_binding_simulation.pdb.gz which can be downloaded by clicking on the filename linked near the top of this page: http://proteopedia.org/wiki/index.php/Image:Hivpi_binding_simulation.pdb.gz My script is: ------------------- # SPINNING WHILE ANIMATING CAUSES CHOPPY RESULTS OR LONG DELAYS IN ANIMATION # ANIMATE BINDING #animation mode loop 1.0 2.0 animation mode once spin off animation on for (var acount = 1; acount < 3; acount = acount + 1) delay 3.5 # leaves time for one animation cycle to complete spin on delay 3.5 # allows for some spinning to occur spin off frame 1 # jump from last frame 21 back to first frame 1 delay 1.0 animation on #message animation cycle @acount end for --------------------- Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Workshops: http://workshops.molviz.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://list.molviz.org Protein Explorer - 3D Visualization: http://proteinexplorer.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
