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] [--win‐
10 dow-id number] [--visual visual] [--delay microseconds] [--wander]
11 [--no-wander] [--spin axes] [--no-spin] [--timeout seconds] [--labels]
12 [--no-labels] [--titles] [--no-titles] [--atoms] [--no-atoms] [--bonds]
13 [--no-bonds] [--shells] [--no-shells] [--molecule file-or-directory]
14 [--verbose] [--wireframe] [--fps]
15
17 The molecule program draws several different representations of mole‐
18 cules. Some common molecules are built in, and it can read PDB (Pro‐
19 tein Data Base) files as input.
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22 molecule accepts the following options:
23 --window
25 Draw on a newly-created window. This is the default.
26 --root Draw on the root window.
28 --window-id number
30 Draw on the specified window.
31 --install
33 Install a private colormap for the window.
34 --visual visual
36 Specify which visual to use. Legal values are the name of a
37 visual class, or the id number (decimal or hex) of a specific
38 visual.
39 --fps Display the current frame rate, CPU load, and polygon count.
41 --verbose
43 Print debugging info on stderr about files being loaded, etc.
44 --wander
46 Move the molecules around the screen.
47 --no-wander
49 Keep the molecule centered on the screen. This is the default.
50 --spin Which axes around which the molecule should spin. The default
52 is "XYZ", meaning rotate it freely in space. "--spin Z" would
53 rotate the molecule in the plane of the screen while not rotat‐
54 ing it into or out of the screen; etc.
55 --no-spin
57 Don't spin it at all: the same as --spin "".
58 --labels
60 Draw labels on the atoms (or the spot where the atoms would
61 be.) This is the default.
62 --no-labels
64 Do not draw labels on the atoms.
65 --titles
67 Print the name of the molecule and its chemical formula at the
68 top of the screen.
69 --no-titles
71 Do not print the molecule name.
72 --atoms Represent the atoms as shaded spheres of appropriate sizes.
74 This is the default.
75 --no-atoms
77 Do not draw spheres for the atoms: only draw bond lines.
78 --bonds Represent the atomic bonds as solid tubes of appropriate thick‐
80 nesses. This is the default.
81 --no-bonds
83 Do not draw the bonds: instead, make the spheres for the atoms
84 be larger, for a "space-filling" representation of the mole‐
85 cule.
86 --shells
88 Draw transparent electron shells around the atoms. This only
89 works if bonds are also being drawn.
90 --no-shells
92 Do not draw electron shells. This is the default.
93 --shell-alpha
95 When drawing shells, how transparent to make them. Default
96 0.4.
97 --wireframe
99 Draw a wireframe rendition of the molecule: this will consist
100 only of single-pixel lines for the bonds, and text labels where
101 the atoms go. This will be very fast.
102 --timeout seconds
104 When using the built-in data set, change to a new molecule ev‐
105 ery this-many seconds. Default is 20 seconds.
106 --molecule file-or-directory
108 Instead of using the built-in molecules, read one from the
109 given file. This file must be in PDB (Protein Data Base) for‐
110 mat. (Note that it's not uncommon for PDB files to contain
111 only the atoms, with no (or little) information about the
112 atomic bonds.)
113 This can also be a directory, in which case, all of the .pdb
115 files in that directory will be loaded. A new one will be dis‐
116 played at random every few seconds (as per the --timeout op‐
117 tion.)
118 When the molecule is too large (bigger than about 30 angstroms from
120 side to side), the --label option will be automatically turned off, be‐
121 cause otherwise, the labels would overlap and completely obscure the
122 display.
123 When the molecule is around 150 angstroms from side to side, wireframe
125 mode will be turned on (because otherwise it would be too slow.)
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128 DISPLAY to get the default host and display number.
129 XENVIRONMENT
131 to get the name of a resource file that overrides the global
132 resources stored in the RESOURCE_MANAGER property.
133 XSCREENSAVER_WINDOW
135 The window ID to use with --root.
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138 X(1), xscreensaver(1)
139 Documentation on the PDB file format:
141 https://web.archive.org/web/20070108054535/https%3A//www.ww‐
143 pdb.org/docs.html
144 https://web.ar‐
145 chive.org/web/19990819134547/https%3A//www.rcsb.org/pdb/docs/for‐
146 mat/pdbguide2.2/guide2.2_frame.html
147 A good source of PDB files:
149 https://www.umass.edu/microbio/rasmol/whereget.htm
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152 Copyright © 2001-2005 by Jamie Zawinski. Permission to use, copy, mod‐
153 ify, distribute, and sell this software and its documentation for any
154 purpose is hereby granted without fee, provided that the above copy‐
155 right notice appear in all copies and that both that copyright notice
156 and this permission notice appear in supporting documentation. No rep‐
157 resentations are made about the suitability of this software for any
158 purpose. It is provided "as is" without express or implied warranty.
159
161 Jamie Zawinski <jwz@jwz.org>
162X Version 11 6.08-1.fc38 (17-Oct-2023) molecule(6x)