Provided by: xscreensaver-gl-extra_5.15-2ubuntu1_i386 bug

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  (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>