NAME

       molecule - draws 3D molecular structures

SYNOPSIS

       molecule   [--display   host:display.screen]   [--window]  [--root]  [--window-id  number]
       [--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.

       --window-id number
               Draw on the specified 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.

       XSCREENSAVER_WINDOW
               The window ID to use with --root.

SEE ALSO

       X(1), xscreensaver(1)

       Documentation on the PDB file format:

       https://web.archive.org/web/20070108054535/https%3A//www.wwpdb.org/docs.html
       https://web.archive.org/web/19990819134547/https%3A//www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

       A good source of PDB files:
       https://www.umass.edu/microbio/rasmol/whereget.htm

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>