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molecule(6)                   XScreenSaver manual                  molecule(6)

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>

X Version 11                  5.34 (24-Oct-2015)                   molecule(6)