PYMOL(1)

💅 pymol(1) — User commands ✨

okay bestie, so this is the manual page for pymol, and the manual name is literally just pymol(1), section 1, user commands. sit down, grab a strawberry, we're doing molecular graphics 💖

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🌸 NAME 🌸

pymol — free and flexible molecular graphics and modelling package. no cap, that's the whole name section. iconic.

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🦋 SYNOPSIS 🦋

pymol [options] [files]

that's it. options, then files. slay.

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✨ DESCRIPTION ✨

so over the years, PyMOL has become, like, a genuinely capable molecular viewer — it supports animations, high-quality rendering, crystallography, and a whole bunch of other common molecular graphics activities. it's giving main character energy fr fr.

it's been adopted by many hundreds (honestly, maybe even thousands) of scientists spread across thirty countries. the reach? global. the vibe? scientific.

but — and this is important — PyMOL is still very much a work in progress, and development is expected to continue for years to come. so like, be nice to it, it's growing 🫶

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🎀 OPTIONS 🎀

these are the options currently supported. yes, all of them. we don't skip 💅

• -2 — start in two-button mouse mode. two buttons, two vibes.
• -c — command line mode, no GUI. this is the one for batch operations, i.e. when you want it to just do the thing with zero window drama.
• -d string — run the pymol command string right upon startup. like a little "hey do this first" 🫡
• -e — start in full-screen mode. immersive. cinematic. ✨
• -f #line — controls display of commands and feedback in OpenGL (0 = off).
• -g file.png — write a PNG file (this happens after evaluating previous arguments, so order matters bestie).
• -i — disable the internal OpenGL GUI (that's the object list, menus, etc.). bye window stuff 👋
• -l file.py — spawn a python program in a new thread.
• -o — disable security protections for session files. ⚠️ yes this is the risky one, don't just casually do this.
• -p — listen for commands on standard input.
• -q — quiet launch. suppress the splash screen & other chatter. introvert mode 🙈
• -r file.py — run a Python program (in __main__) on startup.
• -s script — save commands to this PyMOL script or program file.
• -t — use the Tcl/Tk based external GUI module (pmg_tk).
• -u script — load and append to this PyMOL script or program file.
• -x — disable the external GUI module.
• -B — enable blue-line stereo signal (for Mac stereo).
• -G — start in Game mode. yes, really.
• -M — force mono even when hardware stereo is present.
• -R — launch Greg Landrum's XMLRPC listener.
• -S — force and launch in stereo, if possible.
• -X int -Y int -W int -H int -V int — adjust window geometry. all five of them, together, as a little squad.

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🧚 FILES 🧚

all files you provide will be loaded or run after PyMOL starts. and they can have one of these extensions, each with its own whole personality:

• .pml — PyMOL command script to be run on startup
• .py[cm] — Python program to be run on startup
• .pdb — Protein Data Bank format file to be loaded on startup
• .mmod — Macromodel format to be loaded on startup
• .mol — MDL MOL file to be loaded on startup
• .sdf — MDL SD file to be parsed and loaded on startup
• .xplor — X-PLOR Map file (ASCII) to be loaded on startup
• .ccp4 — CCP4 map file (BINARY) to be loaded on startup
• .cc[12] — ChemDraw 3D cartesian coordinate file
• .pkl — Pickled ChemPy Model (class "chempy.model.Indexed")
• .r3d — Raster3D file
• .cex — CEX file (Metaphorics)
• .top — AMBER topology file
• .crd — AMBER coordinate file
• .rst — AMBER restart file
• .trj — AMBER trajectory
• .pse — PyMOL session file
• .phi — Delphi/Grasp Electrostatic Potential Map

and for a list of options, you can also just type this in the command line of pymol:

help launching

🫶 that's your cheat code.

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👑 COMMANDS 👑

please refer to PyMOL's online documentation at http://www.pymolwiki.org/index.php/Category:Commands or its internal help for a command reference. iykyk 💜

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🌈 AUTHOR 🌈

this manpage was written by Daniel Leidert <daniel.leidert@wgdd.de> for the Debian distribution (but may be used by others). we love a generous king.

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okay so that's the whole thing. source/version is the PYMOL(1) page, dated 2008-05-06 — yes, 2008, a true vintage moment, and it still ate. periodt 💖✨🎀🦋🌸