jmol1

Usage

Overview

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)

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 /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.