molecule(6) XScreenSaver manual molecule(6)

NAME

molecule - draws 3D molecular structures

SYNOPSIS

molecule [--display host:display.screen] [--window] [--root]
[--window-id number] [--visual visual] [--delay microseconds]
[--wander] [--no-wander] [--spin axes] [--no-spin] [--timeout
seconds] [--labels] [--no-labels] [--titles] [--no-titles] [--atoms]
[--no-atoms] [--bonds] [--no-bonds] [--shells] [--no-shells]
[--molecule file-or-directory] [--verbose] [--wireframe] [--fps]

DESCRIPTION

The molecule program draws several different representations of
molecules. Some common molecules are built in, and it can read PDB
(Protein Data Base) files as input.

OPTIONS

molecule accepts the following options:

--window
Draw on a newly-created window. This is the default.

--root Draw on the root window.

--window-id number
Draw on the specified window.

--install
Install a private colormap for the window.

--visual visual
Specify which visual to use. Legal values are the name of a
visual class, or the id number (decimal or hex) of a specific
visual.

--fps Display the current frame rate, CPU load, and polygon count.

--verbose
Print debugging info on stderr about files being loaded, etc.

--wander
Move the molecules around the screen.

--no-wander
Keep the molecule centered on the screen. This is the
default.

--spin Which axes around which the molecule should spin. The
default is "XYZ", meaning rotate it freely in space. "--spin
Z" would rotate the molecule in the plane of the screen while
not rotating it into or out of the screen; etc.

--no-spin
Don't spin it at all: the same as --spin "".

--labels
Draw labels on the atoms (or the spot where the atoms would
be.) This is the default.

--no-labels
Do not draw labels on the atoms.

--titles
Print the name of the molecule and its chemical formula at
the top of the screen.

--no-titles
Do not print the molecule name.

--atoms Represent the atoms as shaded spheres of appropriate sizes.
This is the default.

--no-atoms
Do not draw spheres for the atoms: only draw bond lines.

--bonds Represent the atomic bonds as solid tubes of appropriate
thicknesses. This is the default.

--no-bonds
Do not draw the bonds: instead, make the spheres for the
atoms be larger, for a "space-filling" representation of the
molecule.

--shells
Draw transparent electron shells around the atoms. This only
works if bonds are also being drawn.

--no-shells
Do not draw electron shells. This is the default.

--shell-alpha
When drawing shells, how transparent to make them. Default
0.4.

--wireframe
Draw a wireframe rendition of the molecule: this will consist
only of single-pixel lines for the bonds, and text labels
where the atoms go. This will be very fast.

--timeout seconds
When using the built-in data set, change to a new molecule
every this-many seconds. Default is 20 seconds.

--molecule file-or-directory
Instead of using the built-in molecules, read one from the
given file. This file must be in PDB (Protein Data Base)
format. (Note that it's not uncommon for PDB files to
contain only the atoms, with no (or little) information about
the atomic bonds.)

This can also be a directory, in which case, all of the .pdb
files in that directory will be loaded. A new one will be
displayed at random every few seconds (as per the --timeout
option.)

When the molecule is too large (bigger than about 30 angstroms from
side to side), the --label option will be automatically turned off,
because otherwise, the labels would overlap and completely obscure
the display.

When the molecule is around 150 angstroms from side to side,
wireframe mode will be turned on (because otherwise it would be too
slow.)

ENVIRONMENT

DISPLAY to get the default host and display number.

XENVIRONMENT
to get the name of a resource file that overrides the global
resources stored in the RESOURCE_MANAGER property.

XSCREENSAVER_WINDOW
The window ID to use with --root.

SEE ALSO

X(1), xscreensaver(1)

Documentation on the PDB file format:

https://web.archive.org/web/20070108054535/https%3A//www.wwpdb.org/docs.html
https://web.archive.org/web/19990819134547/https%3A//www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

A good source of PDB files:
https://www.umass.edu/microbio/rasmol/whereget.htm

COPYRIGHT

Copyright (C) 2001-2005 by Jamie Zawinski. Permission to use, copy,
modify, distribute, and sell this software and its documentation for
any purpose is hereby granted without fee, provided that the above
copyright notice appear in all copies and that both that copyright
notice and this permission notice appear in supporting documentation.
No representations are made about the suitability of this software
for any purpose. It is provided "as is" without express or implied
warranty.

AUTHOR

Jamie Zawinski <jwz@jwz.org>

X Version 11 6.09 (07-Jun-2024) molecule(6)