1 .TH XScreenSaver 1 "13-Mar-01" "X Version 11"
3 molecule - draws 3D molecular structures
6 [\-display \fIhost:display.screen\fP] [\-window] [\-root]
7 [\-visual \fIvisual\fP] [\-delay \fImicroseconds\fP]
8 [\-wander] [\-no-wander]
11 [\-timeout \fIseconds\fP]
12 [\-labels] [\-no-labels]
13 [\-titles] [\-no-titles]
14 [\-atoms] [\-no-atoms]
15 [\-bonds] [\-no-bonds]
16 [\-shells] [\-no-shells]
17 [\-molecule \fIfile-or-directory\fP]
22 The \fImolecule\fP program draws several different representations of
23 molecules. Some common molecules are built in, and it can read PDB
24 (Protein Data Base) files as input.
27 accepts the following options:
30 Draw on a newly-created window. This is the default.
33 Draw on the root window.
36 Install a private colormap for the window.
38 .B \-visual \fIvisual\fP\fP
39 Specify which visual to use. Legal values are the name of a visual class,
40 or the id number (decimal or hex) of a specific visual.
43 Display a running tally of how many frames per second are being rendered.
44 In conjunction with \fB\-delay 0\fP, this can be a useful benchmark of
48 Print debugging info on stderr about files being loaded, etc.
51 Move the molecules around the screen.
54 Keep the molecule centered on the screen. This is the default.
57 Which axes around which the molecule should spin. The default is "XYZ",
58 meaning rotate it freely in space. "\fB\-spin Z\fP" would rotate the
59 molecule in the plane of the screen while not rotating it into or out
63 Don't spin it at all: the same as \fB\-spin ""\fP.
66 Draw labels on the atoms (or the spot where the atoms would be.)
70 Do not draw labels on the atoms.
73 Print the name of the molecule and its chemical formula at the top of
77 Do not print the molecule name.
80 Represent the atoms as shaded spheres of appropriate sizes.
84 Do not draw spheres for the atoms: only draw bond lines.
87 Represent the atomic bonds as solid tubes of appropriate thicknesses.
91 Do not draw the bonds: instead, make the spheres for the atoms be
92 larger, for a "space-filling" representation of the molecule.
95 Draw transparent electron shells around the atoms. This only works
96 if bonds are also being drawn.
99 Do not draw electron shells. This is the default.
102 When drawing shells, how transparent to make them. Default 0.4.
105 Draw a wireframe rendition of the molecule: this will consist only of
106 single-pixel lines for the bonds, and text labels where the atoms go.
107 This will be very fast.
109 .B \-timeout \fIseconds\fP
110 When using the built-in data set, change to a new molecule every
111 this-many seconds. Default is 20 seconds.
113 .B \-molecule \fIfile-or-directory\fP
114 Instead of using the built-in molecules, read one from the given file.
115 This file must be in PDB (Protein Data Base) format. (Note that it's
116 not uncommon for PDB files to contain only the atoms, with no (or
117 little) information about the atomic bonds.)
119 This can also be a directory, in which case, all of the .pdb files in
120 that directory will be loaded. A new one will be displayed at random
121 every few seconds (as per the \fI\-timeout\fP option.)
123 When the molecule is too large (bigger than about 30 angstroms from
124 side to side), the \fI\-label\fP option will be automatically turned
125 off, because otherwise, the labels would overlap and completely obscure
128 When the molecule is around 150 angstroms from side to side, wireframe
129 mode will be turned on (because otherwise it would be too slow.)
134 to get the default host and display number.
137 to get the name of a resource file that overrides the global resources
138 stored in the RESOURCE_MANAGER property.
143 Documentation on the PDB file format:
145 http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
147 A good source of PDB files:
149 http://www.sci.ouc.bc.ca/chem/molecule/molecule.html
151 Copyright \(co 2001-2005 by Jamie Zawinski.
152 Permission to use, copy, modify, distribute, and sell this software and
153 its documentation for any purpose is hereby granted without fee,
154 provided that the above copyright notice appear in all copies and that
155 both that copyright notice and this permission notice appear in
156 supporting documentation. No representations are made about the
157 suitability of this software for any purpose. It is provided "as is"
158 without express or implied warranty.
160 Jamie Zawinski <jwz@jwz.org>