JMOL(1)

💖 JMOL(1) — the manual page, but make it a group chat 💖

okay bestie, sit down, hydrate, because we're talking about jmol today and she is that girl 🧚✨

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✨ NAME ✨

jmol — a 3D molecule and crystal viewer 🦋

like, you give her chemical stuff, she spins it around in three dimensions. iconic behaviour honestly.

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🌸 SYNOPSIS 🌸

jmol [options] [file]

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💜 DESCRIPTION 💜

so jmol is a program that is able to view 3D chemical information like molecular structures, vibrations of bonds or animations. no cap. molecules? she sees them. bonds doing a little wiggle? she sees that too. animations? literally her whole thing. 🎀

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👑 OPTIONS 👑

here's the whole menu, bestie, and I mean the whole menu — I'm not skipping a single one because every single flag is a little star ⭐

• -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). so like, how long you gotta hold that animation button before it goes brrr. set it to zero and it just… doesn't. bye 👋
• -b, --backgroundtransparent — transparent background. for when you want your molecule floating in the void, main character style 🌈
• -C, --checkload — check script syntax only - with file loading. vibe check the script, but also bring the file along 🫶
• -c, --check — check script syntax only - no file loading. just the vibe check, no file. periodt.
• -D, --property=value <arg> — supported options are given below. yes bestie, scroll down, they're all listed, I got you 💅
• -d, --debug — debug. when something's acting up and you need the receipts 😭
• -G, --Plugin — jmol is a plugin to some other app. she's not the whole show here, she's a guest star ✨
• -g, --geometry <arg> — window width x height, e.g. -g500x500. you're literally setting the window size. that's it. that's the flag. 📐
• -h, --help — give this help page. hi, this is the help page 👋
• -I, --input — allow piping of input from System.Input. pipe that input in, bestie 🚰
• -i, --silent — silent startup operation. she wakes up quietly, no drama 🌙
• -J, --jmolscript1 <arg> — Jmol script to execute BEFORE -s option. note the BEFORE, capital letters, she means it 🔥
• -j, --jmolscript2 <arg> — Jmol script to execute AFTER -s option. and this one's the AFTER 🦋
• -k, --kiosk — kiosk mode -- no frame. no frame, no chrome, just vibes 🎀
• -L, --nosplash — start with no splash screen. straight to business, no intro sequence 💅
• -l, --list — list commands during script execution. narration on, bestie 🗣️
• -M, --multitouch <arg> — use multitouch interface (requires "sparshui" parameter. yes it needs that parameter, and yes the parenthesis in the original is just like that, I don't make the rules 🤷
• -m, --menu <arg> — menu file to use. pick your menu, queen 👑
• -n, --nodisplay — no display (and also exit when done). she's headless and she knows when to leave 🌸
• -o, --noconsole — no console -- all output to sysout. everything goes to sysout, nothing stays behind 🫶
• -P, --port <arg> — port for JSON/MolecularPlayground-style communication. she's talking to other apps now, networking era 💜
• -p, --printOnly — send only output from print messages to console (implies -i). only the print messages make it through. also, heads up, this implies -i 📢
• -q, --quality <arg> — JPG image quality (1-100; default 75) or PNG image compression (0-9; default 2, maximum compression 9). so for JPG it's quality 1-100 default 75, and for PNG it's compression 0-9 default 2 and the max compression is 9. two different scales, one flag, don't mix them up bestie 😭
• -R, --restricted — restrict local file access. locked down, no wandering 🔒
• -r, --restrictSpt — restrict local file access (allow reading of SPT files). same lock-down energy, but SPT files get a hall pass 🎟️
• -s, --script <arg> — script file to execute or '-' for. yes, that's where the sentence ends in the original, I'm not inventing the rest, I'm just reporting 🫡
• -T, --headlessmaxtime <arg> — headless max time (sec). in seconds, and when time's up, time's up ⏰
• -t, --threaded — independent command thread. she does her own thing on her own thread, independent queen 💅
• -U, --plugin <arg> — plugin to start initially. which plugin gets to go first 🌟
• -w, --write <arg> — CLIP or GIF|JPG|JPG64|PNG|PPM:filename. write it out — either to the clipboard with CLIP, or to a file with one of those formats and a :filename ✍️
• -x, --exit — exit after script (implicit with -n). she dips when the script's done. also heads up: -n already implies this one 👋

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🔥 EXAMPLE 🔥

jmol -ions myscript.spt -w JPEG:myfile.jpg > output.txt

and now the part everybody forgets about: the -D options. they are as follows (defaults in parenthesis) and — and this is the important bit — they must be called preceding '-jar /usr/share/java/Jmol.jar'. like, before. do not pass go. do not collect $200. 💀

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)

note that plugin.dir is (unset) — no default, she's a mystery 🦋 and user.language has a whole little language list with (en_US) as the default, multilingual icon behaviour 🌍

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🎀 FILES 🎀

• ~/.jmol/plugins — Per-user plugin directory. that's where your personal plugins live, in your own lil home folder 🏠

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💖 SEE ALSO 💖

More information about JMol can be found at http://jmol.sourceforge.net/ and in /usr/share/doc/jmol/html (User-Guide). go read, bestie, the User-Guide is right there 📚

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🌸 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). give them their flowers, they wrote this whole thing 💐

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and that's the whole page, bestie. this version was the one dated September 14, 2021, from the JMOL(1) manual — go build something pretty, ily 🫶✨💅