Thank you for the fast answer. The problem i encounter is, that using
the -x option the the skript works perfektly, but using the -n option
the skript halts.
Im executing following Jmol Skript called JWscript:
load auto "file:./out0.xyz"
background [1,1,1]
select z < 13
color "DARKRED"
connect (titanium) (titanium) delete
wireframe 40%
spacefill 22%
zoom 100;
var filename = "out"+("000000"+0)[-5][0]+".pov"
write POVRAY @filename
Using jmol-12 -g800x600 -s JWscript -x it produces the .pov and .pov.ini
file and exits, while using jmol-12 -g800x600 -s JWscript -n it just
produces the .pov file and stops.
Any sugestions for a solution would be appreciated.
Stephan
Am 07.02.2014 14:13, schrieb Robert Hanson:
> Stephan,
>
> Yes, absolutely. Everything you can do with scripts you can do without
> any graphical interface at all. The program to run is JmolData.jar. It
> is completely "headless" and is designed for doing exactly what you
> describe. (You can do the same with Jmol.jar or JmolData.jar, but
> JmolData.jar is faster because it doesn't have any graphics system
> overhead.)
>
> You basically send it a script, and it does its work and exits. The
> DOS batch file I use for it is named JmolData.bat and looks like this:
>
>
> @echo off
> java -Xmx512m -jar "..\workspace\jmol\build\JmolData.jar" %1 %2 %3 %4
> %5 %6 %7 %8 %9
>
> So then if I type
>
> JmolData -h
>
> I get the help info:
>
> usage: Jmol
> -o,--noconsole no console -- all output to sysout
> -c,--check check script syntax only - no file loading
> -k,--kiosk kiosk mode -- no frame
> -C,--checkload check script syntax only - with file loading
> -s,--script script file to execute or '-' for System.in
> -q,--quality JPG image quality (1-100; default 75) or PNG
> image compression (0-9; default 2,
> maximum compression 9)
> -g,--geometry window width x height, e.g. -g500x500
> -p,--printOnly send only output from print messages to
> console (implies -i)
> -x,--exit exit after script (implicit with -n)
> -j,--jmolscript2 Jmol script to execute AFTER -s option
> -J,--jmolscript1 Jmol script to execute BEFORE -s option
> -P,--port port for JSON/MolecularPlayground-style
> communication
> -D <property=value> supported options are given below
> -I,--input allow piping of input from System.Input
> -L,--nosplash start with no splash screen
> -M,--multitouch use multitouch interface (requires
> "sparshui" parameter
> -R,--restricted restrict local file access
> -T,--headlessmaxtime headless max time (sec)
> -b,--backgroundtransparent transparent background
> -d,--debug debug
> -h,--help give this help page
> -i,--silent silent startup operation
> -l,--list list commands during script execution
> -m,--menu menu file to use
> -n,--nodisplay no display (and also exit when done)
> -r,--restrictSpt restrict local file access (allow reading of
> SPT files)
> -t,--threaded independent command thread
> -w,--write CLIP or GIF|JPG|JPG64|PNG|PPM:filename
>
> For example:
>
> Jmol -ions myscript.spt -w JPEG:myfile.jpg > output.txt
>
> The -D options are as follows (defaults in parenthesis) and must be
> called preceding '-jar Jmol.jar':
>
> cdk.debugging=[true|false] (false)
> cdk.debug.stdout=[true|false] (false)
> display.speed=[fps|ms] (ms)
> logger.debug=[true|false] (false)
> logger.error=[true|false] (true)
> logger.fatal=[true|false] (true)
> logger.info <http://logger.info>=[true|false] (true)
> logger.logLevel=[true|false] (false)
> logger.warn=[true|false] (true)
> plugin.dir (unset)
>
> user.language=[ca|cs|de|en_GB|en_US|es|fr|hu|it|ko|nl|pt_BR|tr|zh_TW]
> (en_US)
>
>
> (I notice a fault there in that the help refers to "Jmol.jar" even
> though I started JmolData.jar.) Basically this is just Jmol without
> any graphical user interface. Everything is the same exactly.
>
> Bob Hanson
>
>
>
> On Fri, Feb 7, 2014 at 5:20 AM, Stephan Pfadenhauer <[email protected]
> <mailto:[email protected]>> wrote:
>
> Hi,
>
> I'm using a bash skript to generate movies from xyz files with
> multiple
> frames. I'm using Jmol for rotation, deleting of bonds and coloring
> atoms with a skript and generating a pov file. Is there a
> possibility of
> using the Jmol comandline only, without the Jmol Window poping up?
>
> Stephan
>
>
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Annaberger Strasse 240
09125 Chemnitz
Telefon: 0371 5347591
Email: [email protected]
Internet: http://www.matcalc.de
Geschaeftsfuehrer: Dr. Philipp Plaenitz
Gesellschafter:
Prof. Dr. Christian Radehaus
Dr. Philipp Plaenitz
Amtsgericht Chemnitz: HRB 25386
Diese e-mail kann Betriebs- oder Geschaeftsgeheimnisse oder sonstige
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