Home Man
Today's Posts

Linux & Unix Commands - Search Man Pages

RedHat 9 (Linux i386) - man page for molecule (redhat section 1)

XScreenSaver(1) 		     General Commands Manual			  XScreenSaver(1)

       molecule - draws 3D moleclear structures

       gltext [-display host:display.screen] [-window] [-root] [-visual visual] [-delay microsec-
       onds] [-fps] [-wander] [-no-wander] [-spin axes]  [-no-spin]  [-wire]  [-timeout  seconds]
       [-labels]  [-no-labels]	[-titles]  [-no-titles] [-atoms] [-no-atoms] [-bonds] [-no-bonds]
       [-molecule filename]

       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.

       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 visual.

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

       -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 rotating 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

	       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 thicknesses.  This is the

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

       -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 sec-
	       onds.  Default is 20 seconds.

       -molecule filename
	       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

       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  over-
       lap 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.)

       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  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.

       Jamie Zawinski <jwz@jwz.org>

X Version 11				    13-Mar-01				  XScreenSaver(1)

All times are GMT -4. The time now is 02:07 AM.

Unix & Linux Forums Content Copyrightę1993-2018. All Rights Reserved.
Show Password