if you really really really would need to perform operations on all the frames, you could also split the xyz before reading them in jmol:
Say, if you have 10000 atoms in your system, and you want to split your trajectory in batches of 100 frames, you could use the bash command split: p...@mypc:~> split -a 4 -d -l 1000200 trajectory.xyz trajectory.xyz.split. (in xyz there are probably 2 comment lines in each frame) this gives you trajectory.xyz.split.0001 trajectory.xyz.split.0002 etc. You could then load them separately or use a jmol script greetings, Pim On 6/19/09, Nicolas Bock <[email protected]> wrote: > Hi Bob, > > thanks for clarifying this. > > nick > > > On Thu, Jun 18, 2009 at 22:12, Robert Hanson <[email protected]> wrote: > >> The maximum number of models in a file is limited by the format for >> describing models: >> >> x.y >> >> where x is the file number and y is the model number in the file. The >> limitation on y is 9999. >> >> If you have more than that number of models in a single file, you should >> consider using a trajectory and probably load only, say, every 5th model. >> >> Bob >> >> >> On Thu, Jun 18, 2009 at 8:53 AM, Nicolas Bock >> <[email protected]>wrote: >> >>> Hello list, >>> >>> I am trying to read an xyz file into Jmol that has a lot of frames. Jmol >>> doesn't load the file and on the java console I get this error message: >>> >>> 34106 models in this collection. Use getProperty "modelInfo" or >>> getProperty "auxiliaryInfo" to inspect them. >>> Exception in thread "QueueThread0" >>> java.lang.ArrayIndexOutOfBoundsException: -32768 >>> at org.jmol.modelset.ModelLoader.iterateOverAllNewAtoms(Unknown >>> Source) >>> at org.jmol.modelset.ModelLoader.initializeModelSet(Unknown Source) >>> at org.jmol.modelset.ModelLoader.<init>(Unknown Source) >>> at org.jmol.viewer.ModelManager.setClientFile(Unknown Source) >>> at org.jmol.viewer.Viewer.openClientFile(Unknown Source) >>> at org.jmol.viewer.Viewer.getOpenFileError(Unknown Source) >>> at org.jmol.viewer.Eval.load(Unknown Source) >>> at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) >>> at org.jmol.viewer.Eval.runEval(Unknown Source) >>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) >>> at >>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown >>> Source) >>> at >>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown >>> Source) >>> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown >>> Source) >>> at java.lang.Thread.run(Thread.java:619) >>> >>> My completely uneducated guess is that Jmol uses a short signed int for >>> the number of models and that's why it's failing, but of course I might >>> be >>> completely off here. What is the maximum number of models an xyz file can >>> have? Can one raise this limit? >>> >>> Thanks already, nick >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Crystal Reports - New Free Runtime and 30 Day Trial >>> Check out the new simplified licensing option that enables unlimited >>> royalty-free distribution of the report engine for externally facing >>> server and web deployment. >>> http://p.sf.net/sfu/businessobjects >>> _______________________________________________ >>> Jmol-users mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> 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 >> >> >> ------------------------------------------------------------------------------ >> Crystal Reports - New Free Runtime and 30 Day Trial >> Check out the new simplified licensing option that enables unlimited >> royalty-free distribution of the report engine for externally facing >> server and web deployment. >> http://p.sf.net/sfu/businessobjects >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > -- Greetings, Pim http://www.molmod.com ------------------------------------------------------------------------------ Are you an open source citizen? Join us for the Open Source Bridge conference! Portland, OR, June 17-19. Two days of sessions, one day of unconference: $250. Need another reason to go? 24-hour hacker lounge. Register today! http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
