Linux and UNIX Man Pages

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 microseconds] [-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 (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 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. -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. -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 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 bonds.) 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.)
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.
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 <> X Version 11 13-Mar-01 XScreenSaver(1)