James, a few suggestions: First, you have to be in the frame of the model you want the isosurface for before issuing the isosurface command. And you need to give each isosurface a distinct identifier. So:
frame 1 frame 1 isosurface a1 0.05 sign blue red "MO1a.cube";color isosurface translucent; frame 2 isosurface a2 0.05 sign blue red "MO1b.cube";color isosurface translucent; frame 3 isosurface a3 0.05 sign blue red "MO1c.cube";color isosurface translucent; frame 4 isosurface a4 0.05 sign blue red "MO1d.cube";color isosurface translucent; Animation is probably not going to work with cube files. The files are so huge, and the calculation is very intense. You might get away with it on a local machine, but this would never work in an applet. Consider JVXL files instead. Do as you have done, above, using the Jmol application (not the applet), and then do this: frame 1;write isosurface "mo1a.jvxl" frame 2;write isosurface "mo1b.jvxl" frame 3;write isosurface "mo1c.jvxl" frame 4;write isosurface "mo1d.jvxl" Now you have a set of files that can be delivered over the web very quickly: load mo1a.jvxl;isosurface "";color isosurface translucent load append mo1b.jvxl;isosurface "";color isosurface translucent load append mo1c.jvxl;isosurface "";color isosurface translucent load append mo1d.jvxl;isosurface "";color isosurface translucent should do the trick. Now your animation should load and run smoothly. If you have a coordinate file that is better than a cube file, you could use that for the load instead. Perhaps: load myfile.mol;isosurface "mo1a.jvxl";color isosurface translucent load append myfle.mol;isosurface "mo1b.jvxl";color isosurface translucent load append myfile.mol;isosurface "mo1c.jvxl";color isosurface translucent load append myfile.mol;isosurface "mo1d.jvxl";color isosurface translucent Bob James Keeler wrote: >I am a novice user of Jmol, and need some help please with the following. > >(1) I have a series of .cube files, each of which contains a single >structure and a single MO. > >(2) I wish to animate a sequence using these structures and MOs >(rendered as isosurfaces). > >(3) My attempt is the following script: > >zap; >load files "MO1a.cube" "MO1b.cube" "MO1c.cube" "MO1d.cube"; >moveto 0.0 9 -997 82 82.92; >spacefill 10%;select all;connect 1.0 (selected)(selected) >create;wireframe 5;color bonds grey; >isosurface both 0.05 sign blue red "";color isosurface translucent; >animation mode once; >animation fps 1; >frame range 1.1 4.1; >frame play; > >(4) Thus puts the required isosurface on the first frame, but >although the molecule appears in frames 2, 3 and 4, no isosurfaces appear. > >(5) If it is necessary, I can merge all the data into one .cube file. > >I would appreciate some help and guidance with this. > >Thank you in advance. > >James Keeler > >James Keeler, Director of Teaching >Department of Chemistry, University of Cambridge >Lensfield Rd, Cambridge CB2 1EW > >Tel. (01223) 336428 Secretary (Henneli Greyling) 336480 FAX 336362 >WWW: www-keeler.ch.cam.ac.uk and www-teach.ch.cam.ac.uk > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
