molecule man page on SuSE
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molecule(6x) XScreenSaver manual molecule(6x)
NAME
molecule - draws 3D molecular structures
SYNOPSIS
molecule [-display host:display.screen] [-window] [-root] [-visual vis‐
ual] [-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] [-mol‐
ecule file-or-directory] [-verbose] [-wireframe] [-fps]
DESCRIPTION
The molecule program draws several different representations of mole‐
cules. Some common molecules are built in, and it can read PDB (Pro‐
tein 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.
-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 rotat‐
ing 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 thick‐
nesses. 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 mole‐
cule.
-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) for‐
mat. (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 dis‐
played 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.
SEE ALSO
X(1), xscreensaver(1)
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
COPYRIGHT
Copyright © 2001-2005 by Jamie Zawinski. Permission to use, copy, mod‐
ify, distribute, and sell this software and its documentation for any
purpose is hereby granted without fee, provided that the above copy‐
right notice appear in all copies and that both that copyright notice
and this permission notice appear in supporting documentation. No rep‐
resentations 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 5.07 (10-Aug-2008) molecule(6x)
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