Switch to SpeakEasy.net DSL

The Modular Manual Browser

Home Page
Manual: (Debian-3.1)
Apropos / Subsearch:
optional field

XScreenSaver(6x)                                              XScreenSaver(6x)

       molecule - draws 3D moleclear structures

       gltext  [-display  host:display.screen] [-window] [-root] [-visual vis-
       ual] [-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]

       The  molecule  program draws several different representations of mole-
       cules.  Some common molecules are built in, and it can read  PDB  (Pro-
       tein Data Base) files as input.

       molecule accepts the following options:

       -window Draw on a newly-created window.  This is the default.

       -root   Draw on the root window.

               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

       -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.

               Print debugging info on stderr about files being loaded, etc.

       -wander Move the molecules around the screen.

               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.

               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.

               Do not draw labels on the atoms.

       -titles Print  the name of the molecule and its chemical formula at the
               top of the screen.

               Do not print the molecule name.

       -atoms  Represent the atoms as shaded  spheres  of  appropriate  sizes.
               This is the default.

               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.

               Do not draw the bonds: instead, make the spheres for the  atoms
               be  larger,  for  a "space-filling" representation of the mole-

       -shells Draw transparent electron shells around the atoms.   This  only
               works if bonds are also being drawn.

               Do not draw electron shells.  This is the default.

               When  drawing  shells,  how  transparent to make them.  Default

       -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

       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

       When  the molecule is around 150 angstroms from side to side, wireframe
       mode will be turned on (because otherwise it would be too slow.)

       DISPLAY to get the default host and display number.

               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:


       A good source of PDB files:


       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-

       Jamie Zawinski <jwzATjwz.org>

X Version 11                  4.21 (01-Mar-2005)              XScreenSaver(6x)