Also, Jmol's load TRAJECTORY command allows you to use the same idea to load
only specific trajectories from a set using the first, last, and "stride"
familiar to AMBER users.
load TRAJECTORY {first last stride} or ({i j k:l m..}) "filename"*
Loads the specified subset of models from the file as a trajectory.
**In the first syntax, first and last models along with a "stride" (step)
are specified. Models are then read using an equivalent of for (i = first; i
<= last; i = i + stride). Numbers start with 0 for the first model; -1 for
last indicates "to the end of the file." For example, load MODELS {0 10 2}
"..." would load six models, models 0, 2, 4, 6, 8, and 10.*
*
*So, Pim, can you explain those split command parameters? How do they
indicate to do this?
Bob
On Tue, Jun 23, 2009 at 4:12 AM, pim schravendijk
<[email protected]>wrote:
> 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
>
>
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--
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
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