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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 rotat-
                ing 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 thick-
                nesses.  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) for-
                mat.  (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 dis-
                played 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.
        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 war-
        ranty.
 

AUTHOR

        Jamie Zawinski <jwz@jwz.org>