+++ /dev/null
-.TH XScreenSaver 1 "13-Mar-01" "X Version 11"
-.SH NAME
-molecule - draws 3D molecular structures
-.SH SYNOPSIS
-.B molecule
-[\-display \fIhost:display.screen\fP] [\-window] [\-root]
-[\-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 \-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.
-.SH SEE ALSO
-.BR X (1),
-.BR xscreensaver (1)
-.PP
-Documentation on the PDB file format:
-
- http://www.wwpdb.org/docs.html
- http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
-
-A good source of PDB files:
-
- http://www.umass.edu/microbio/rasmol/whereget.htm
- http://www.wwpdb.org/docs.html
-.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>
projects / xscreensaver / blobdiff