XScreenSaver(1)XScreenSaver(1)NAMEmolecule - draws 3D moleclear structures
SYNOPSIS
gltext [-display host:display.screen] [-window] [-root]
[-visual visual] [-delay microseconds] [-fps] [-wander]
[-no-wander] [-spin axes] [-no-spin] [-wire] [-timeout
seconds] [-labels] [-no-labels] [-titles] [-no-titles]
[-atoms] [-no-atoms] [-bonds] [-no-bonds] [-molecule file_
name]
DESCRIPTION
The molecule program draws several different representa
tions of molecules. Some common molecules are built in,
and it can read PDB (Protein Data Base) files as input.
OPTIONSmolecule 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 a running tally of how many frames per
second are being rendered. In conjunction with
-delay 0, this can be a useful benchmark of your
GL performance.
-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 appropri
ate 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.
-wire 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 filename
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.)
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_MAN
AGER property.
SEE ALSOX(1), xscreensaver(1)
Documentation on the PDB file format:
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
A good source of PDB files:
http://www.sci.ouc.bc.ca/chem/molecule/molecule.html
COPYRIGHT
Copyright 2001 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 13-Mar-01 XScreenSaver(1)
