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molecule - draws 3D molecular structures
molecule [-display host:display.screen] [-window] [-root] [-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]
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.
molecule accepts the following options:
-window Draw on a newly-created window. This is the default.
-root Draw on the root window.
Install a private colormap for the window.
Specify which visual to use. Legal values are the name of a
visual class, or the id number (decimal or hex) of a specific
-fps Display the current frame rate, CPU load, and polygon count.
Print debugging info on stderr about files being loaded, etc.
-wander Move the molecules around the screen.
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 rotat-
ing it into or out of the screen; etc.
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.
Do not draw labels on the atoms.
-titles Print the name of the molecule and its chemical formula at the
top of the screen.
Do not print the molecule name.
-atoms Represent the atoms as shaded spheres of appropriate sizes.
This is the default.
Do not draw spheres for the atoms: only draw bond lines.
-bonds Represent the atomic bonds as solid tubes of appropriate thick-
nesses. This is the default.
Do not draw the bonds: instead, make the spheres for the atoms
be larger, for a "space-filling" representation of the
-shells Draw transparent electron shells around the atoms. This only
works if bonds are also being drawn.
Do not draw electron shells. This is the default.
When drawing shells, how transparent to make them. Default
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.
When using the built-in data set, change to a new molecule
every this-many seconds. Default is 20 seconds.
Instead of using the built-in molecules, read one from the
given file. This file must be in PDB (Protein Data Base) for-
mat. (Note that it's not uncommon for PDB files to contain
only the atoms, with no (or little) information about the
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 dis-
played at random every few seconds (as per the -timeout
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
When the molecule is around 150 angstroms from side to side, wireframe
mode will be turned on (because otherwise it would be too slow.)
DISPLAY to get the default host and display number.
to get the name of a resource file that overrides the global
resources stored in the RESOURCE_MANAGER property.
Documentation on the PDB file format:
A good source of PDB files:
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 war-
Jamie Zawinski <firstname.lastname@example.org>