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>

X Version 11                                   6.08 (10-Oct-2023)                                   molecule(6x)