molecule(6x)							XScreenSaver manual						      molecule(6x)

NAME

       molecule - draws 3D molecular structures

SYNOPSIS

       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]

DESCRIPTION

       The  molecule  program draws several different representations of molecules.  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 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 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 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.

       -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) 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 -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  (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 warranty.

AUTHOR

       Jamie Zawinski <jwz@jwz.org>

X Version 11							5.15 (28-Sep-2011)						      molecule(6x)