molecule



XScreenSaver(1)                                                XScreenSaver(1)




NAME

       molecule - draws 3D moleclear structures


SYNOPSIS

       gltext   [-display   host:display.screen]  [-window]  [-root]  [-visual
       visual] [-delay  microseconds]  [-fps]  [-wander]  [-no-wander]  [-spin
       axes]  [-no-spin] [-wire] [-verbose] [-timeout seconds] [-labels] [-no-
       labels] [-titles]  [-no-titles]  [-atoms]  [-no-atoms]  [-bonds]  [-no-
       bonds] [-shells] [-no-shells] [-molecule file-or-directory]


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 a running tally of how many frames per second are being
               rendered.  In conjunction with -delay 0, this can be  a  useful
               benchmark of your GL performance.

       -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.

       -wire   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.


SEE ALSO

       X(1), xscreensaver(1)

       Documentation on the PDB file format:

           http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

       A good source of PDB files:

           http://www.sci.ouc.bc.ca/chem/molecule/molecule.html


COPYRIGHT

       Copyright © 2001-2005 by Jamie Zawinski.  Permission to use, copy, mod-
       ify, distribute, and sell this software and its documentation  for  any
       purpose  is  hereby  granted without fee, provided that the above copy-
       right notice appear in all copies and that both that  copyright  notice
       and this permission notice appear in supporting documentation.  No rep-
       resentations 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                       13-Mar-01                   XScreenSaver(1)

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