This does not surprise me at all. Spin and animation are two separate
threads, both of which force updates. I don't think they are compatible.
On Mon, Aug 31, 2009 at 4:51 PM, Eric Martz <[email protected]>wrote:
> 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
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> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
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phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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