.TH molecule 6 "6.09 (07-Jun-2024)" "X Version 11" "XScreenSaver manual"
.SH NAME
molecule \- draws 3D molecular structures
.SH SYNOPSIS
.B molecule
[\-\-display \fIhost:display.screen\fP] [\-\-window] [\-\-root]
[\-\-window\-id \fInumber\fP]
[\-\-visual \fIvisual\fP] [\-\-delay \fImicroseconds\fP]
[\-\-wander] [\-\-no-wander]
[\-\-spin \fIaxes\fP]
[\-\-no-spin]
[\-\-timeout \fIseconds\fP]
[\-\-labels] [\-\-no-labels]
[\-\-titles] [\-\-no-titles]
[\-\-atoms] [\-\-no-atoms]
[\-\-bonds] [\-\-no-bonds]
[\-\-shells] [\-\-no-shells]
[\-\-molecule \fIfile-or-directory\fP]
[\-\-verbose]
[\-\-wireframe]
[\-\-fps]
.SH DESCRIPTION
The \fImolecule\fP program draws several different representations of
molecules.  Some common molecules are built in, and it can read PDB
(Protein Data Base) files as input.
.SH OPTIONS
.I molecule
accepts the following options:
.TP 8
.B \-\-window
Draw on a newly-created window.  This is the default.
.TP 8
.B \-\-root
Draw on the root window.
.TP 8
.B \-\-window\-id \fInumber\fP
Draw on the specified window.
.TP 8
.B \-\-install
Install a private colormap for the window.
.TP 8
.B \-\-visual \fIvisual\fP\fP
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.
.TP 8
.B \-\-fps
Display the current frame rate, CPU load, and polygon count.
.TP 8
.B \-\-verbose
Print debugging info on stderr about files being loaded, etc.
.TP 8
.B \-\-wander
Move the molecules around the screen.
.TP 8
.B \-\-no\-wander
Keep the molecule centered on the screen.  This is the default.
.TP 8
.B \-\-spin
Which axes around which the molecule should spin.  The default is "XYZ",
meaning rotate it freely in space.  "\fB\-\-spin Z\fP" would rotate the
molecule in the plane of the screen while not rotating it into or out
of the screen; etc.
.TP 8
.B \-\-no\-spin
Don't spin it at all: the same as \fB\-\-spin ""\fP.
.TP 8
.B \-\-labels
Draw labels on the atoms (or the spot where the atoms would be.)
This is the default.
.TP 8
.B \-\-no\-labels
Do not draw labels on the atoms.
.TP 8
.B \-\-titles
Print the name of the molecule and its chemical formula at the top of
the screen.
.TP 8
.B \-\-no\-titles
Do not print the molecule name.
.TP 8
.B \-\-atoms
Represent the atoms as shaded spheres of appropriate sizes.
This is the default.
.TP 8
.B \-\-no\-atoms
Do not draw spheres for the atoms: only draw bond lines.
.TP 8
.B \-\-bonds
Represent the atomic bonds as solid tubes of appropriate thicknesses.
This is the default.
.TP 8
.B \-\-no\-bonds
Do not draw the bonds: instead, make the spheres for the atoms be
larger, for a "space-filling" representation of the molecule.
.TP 8
.B \-\-shells
Draw transparent electron shells around the atoms.  This only works
if bonds are also being drawn.
.TP 8
.B \-\-no\-shells
Do not draw electron shells.  This is the default.
.TP 8
.B \-\-shell\-alpha
When drawing shells, how transparent to make them.  Default 0.4.
.TP 8
.B \-\-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.
.TP 8
.B \-\-timeout \fIseconds\fP
When using the built-in data set, change to a new molecule every
this-many seconds.  Default is 20 seconds.
.TP 8
.B \-\-molecule \fIfile-or-directory\fP
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 \fI\-\-timeout\fP option.)
.PP
When the molecule is too large (bigger than about 30 angstroms from
side to side), the \fI\-\-label\fP 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.)
.SH ENVIRONMENT
.PP
.TP 8
.B DISPLAY
to get the default host and display number.
.TP 8
.B XENVIRONMENT
to get the name of a resource file that overrides the global resources
stored in the RESOURCE_MANAGER property.
.TP 8
.B XSCREENSAVER_WINDOW
The window ID to use with \fI\-\-root\fP.
.SH SEE ALSO
.BR X (1),
.BR xscreensaver (1)
.PP
Documentation on the PDB file format:
.P
https://web.archive.org/web/20070108054535/https%3A//www.wwpdb.org/docs.html
.br
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:
.br
https://www.umass.edu/microbio/rasmol/whereget.htm
.SH COPYRIGHT
Copyright \(co 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.
.SH AUTHOR
Jamie Zawinski <jwz@jwz.org>