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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 (Protein 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 © 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>