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=[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 <s...@matcalc.de> 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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Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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