NAME¶

jmol - 3D Viewer for chemical structures

SYNOPSIS¶

jmol [options]

DESCRIPTION¶

Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.

OPTIONS¶

-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

EXAMPLES¶

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)

SEE ALSO¶

java(1)

For more information, see also <http://jmol.sourceforge.net/>

BUGS¶

No known bugs.

AUTHOR¶

Jmol authors (jmol-developers@lists.sf.net)