---
name: "jmol"
section: "1"
platform: "linux"
package: "jmol"
version: "16.2.33+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/jmol"
---

# jmol(1)

3D molecule and crystal viewer

## 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 \<egonw@users.sourceforge.net\>, Daniel Leidert \<daniel.leidert@wgdd.de\> and Pierre Gruet \<pgt@debian.org\> for the Debian GNU/Linux distribution (but may be used by others).