NAME
jmol - 3D molecule and crystal viewer
SYNOPSIS
jmol [options] [file]
DESCRIPTION
jmol is a program that is able to view 3D chemical information like molecular structures, vibrations of bonds or animations.
OPTIONS
- -a,--autoanimationdelay <arg>
-
delay time in seconds for press-and-hold operation of toolbar animation buttons (default 0.2; numbers > 10 assumed to be milliseconds; set to 0 to disable)
- -b,--backgroundtransparent
-
transparent background
- -C,--checkload
-
check script syntax only - with file loading
- -c,--check
-
check script syntax only - no file loading
- -D,--property=value <arg>
-
supported options are given below
- -d,--debug
-
debug
- -G,--Plugin
-
jmol is a plugin to some other app
- -g,--geometry <arg>
-
window width x height, e.g. -g500x500
- -h,--help
-
give this help page
- -I,--input
-
allow piping of input from System.Input
- -i,--silent
-
silent startup operation
- -J,--jmolscript1 <arg>
-
Jmol script to execute BEFORE -s option
- -j,--jmolscript2 <arg>
-
Jmol script to execute AFTER -s option
- -k,--kiosk
-
kiosk mode -- no frame
- -L,--nosplash
-
start with no splash screen
- -l,--list
-
list commands during script execution
- -M,--multitouch <arg>
-
use multitouch interface (requires "sparshui" parameter
- -m,--menu <arg>
-
menu file to use
- -n,--nodisplay
-
no display (and also exit when done)
- -o,--noconsole
-
no console -- all output to sysout
- -P,--port <arg>
-
port for JSON/MolecularPlayground-style communication
- -p,--printOnly
-
send only output from print messages to console (implies -i)
- -q,--quality <arg>
-
JPG image quality (1-100; default 75) or PNG image compression (0-9; default 2, maximum compression 9)
- -R,--restricted
-
restrict local file access
- -r,--restrictSpt
-
restrict local file access (allow reading of SPT files)
- -s,--script <arg>
-
script file to execute or '-' for
- -T,--headlessmaxtime <arg>
-
headless max time (sec)
- -t,--threaded
-
independent command thread
- -U,--plugin <arg>
-
plugin to start initially
- -w,--write <arg>
-
CLIP or GIF|JPG|JPG64|PNG|PPM:filename
- -x,--exit
-
exit after script (implicit with -n)
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 /usr/share/java/Jmol.jar':
- 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)
FILES
- ~/.jmol/plugins
-
Per-user plugin directory.
SEE ALSO
More information about JMol can be found at http://jmol.sourceforge.net/ and in /usr/share/doc/jmol/html (User-Guide).
AUTHORS
This manual page was written by Egon Willighagen <[email protected]>, Daniel Leidert <[email protected]> and Pierre Gruet <[email protected]> for the Debian GNU/Linux distribution (but may be used by others).