1molecule(6x) XScreenSaver manual molecule(6x)
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6 molecule - draws 3D molecular structures
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9 molecule [-display host:display.screen] [-window] [-root] [-visual vis‐
10 ual] [-delay microseconds] [-wander] [-no-wander] [-spin axes] [-no-
11 spin] [-timeout seconds] [-labels] [-no-labels] [-titles] [-no-titles]
12 [-atoms] [-no-atoms] [-bonds] [-no-bonds] [-shells] [-no-shells] [-mol‐
13 ecule file-or-directory] [-verbose] [-wireframe] [-fps]
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16 The molecule program draws several different representations of mole‐
17 cules. Some common molecules are built in, and it can read PDB (Pro‐
18 tein Data Base) files as input.
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21 molecule accepts the following options:
22 -window Draw on a newly-created window. This is the default.
24 -root Draw on the root window.
26 -install
28 Install a private colormap for the window.
29 -visual visual
31 Specify which visual to use. Legal values are the name of a
32 visual class, or the id number (decimal or hex) of a specific
33 visual.
34 -fps Display a running tally of how many frames per second are being
36 rendered. In conjunction with -delay 0, this can be a useful
37 benchmark of your GL performance.
38 -verbose
40 Print debugging info on stderr about files being loaded, etc.
41 -wander Move the molecules around the screen.
43 -no-wander
45 Keep the molecule centered on the screen. This is the default.
46 -spin Which axes around which the molecule should spin. The default
48 is "XYZ", meaning rotate it freely in space. "-spin Z" would
49 rotate the molecule in the plane of the screen while not rotat‐
50 ing it into or out of the screen; etc.
51 -no-spin
53 Don't spin it at all: the same as -spin "".
54 -labels Draw labels on the atoms (or the spot where the atoms would
56 be.) This is the default.
57 -no-labels
59 Do not draw labels on the atoms.
60 -titles Print the name of the molecule and its chemical formula at the
62 top of the screen.
63 -no-titles
65 Do not print the molecule name.
66 -atoms Represent the atoms as shaded spheres of appropriate sizes.
68 This is the default.
69 -no-atoms
71 Do not draw spheres for the atoms: only draw bond lines.
72 -bonds Represent the atomic bonds as solid tubes of appropriate thick‐
74 nesses. This is the default.
75 -no-bonds
77 Do not draw the bonds: instead, make the spheres for the atoms
78 be larger, for a "space-filling" representation of the mole‐
79 cule.
80 -shells Draw transparent electron shells around the atoms. This only
82 works if bonds are also being drawn.
83 -no-shells
85 Do not draw electron shells. This is the default.
86 -shell-alpha
88 When drawing shells, how transparent to make them. Default
89 0.4.
90 -wireframe
92 Draw a wireframe rendition of the molecule: this will consist
93 only of single-pixel lines for the bonds, and text labels where
94 the atoms go. This will be very fast.
95 -timeout seconds
97 When using the built-in data set, change to a new molecule
98 every this-many seconds. Default is 20 seconds.
99 -molecule file-or-directory
101 Instead of using the built-in molecules, read one from the
102 given file. This file must be in PDB (Protein Data Base) for‐
103 mat. (Note that it's not uncommon for PDB files to contain
104 only the atoms, with no (or little) information about the
105 atomic bonds.)
106 This can also be a directory, in which case, all of the .pdb
108 files in that directory will be loaded. A new one will be dis‐
109 played at random every few seconds (as per the -timeout
110 option.)
111 When the molecule is too large (bigger than about 30 angstroms from
113 side to side), the -label option will be automatically turned off,
114 because otherwise, the labels would overlap and completely obscure the
115 display.
116 When the molecule is around 150 angstroms from side to side, wireframe
118 mode will be turned on (because otherwise it would be too slow.)
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121 DISPLAY to get the default host and display number.
122 XENVIRONMENT
124 to get the name of a resource file that overrides the global
125 resources stored in the RESOURCE_MANAGER property.
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128 X(1), xscreensaver(1)
129 Documentation on the PDB file format:
131 http://www.wwpdb.org/docs.html
133 http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
134 A good source of PDB files:
136 http://www.umass.edu/microbio/rasmol/whereget.htm
138 http://www.wwpdb.org/docs.html
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141 Copyright © 2001-2005 by Jamie Zawinski. Permission to use, copy, mod‐
142 ify, distribute, and sell this software and its documentation for any
143 purpose is hereby granted without fee, provided that the above copy‐
144 right notice appear in all copies and that both that copyright notice
145 and this permission notice appear in supporting documentation. No rep‐
146 resentations are made about the suitability of this software for any
147 purpose. It is provided "as is" without express or implied warranty.
148
150 Jamie Zawinski <jwz@jwz.org>
151X Version 11 5.05-3 (06-Apr-2008) molecule(6x)