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 the current frame rate, CPU load, and polygon count.
36 -verbose
38 Print debugging info on stderr about files being loaded, etc.
39 -wander Move the molecules around the screen.
41 -no-wander
43 Keep the molecule centered on the screen. This is the default.
44 -spin Which axes around which the molecule should spin. The default
46 is "XYZ", meaning rotate it freely in space. "-spin Z" would
47 rotate the molecule in the plane of the screen while not rotat‐
48 ing it into or out of the screen; etc.
49 -no-spin
51 Don't spin it at all: the same as -spin "".
52 -labels Draw labels on the atoms (or the spot where the atoms would
54 be.) This is the default.
55 -no-labels
57 Do not draw labels on the atoms.
58 -titles Print the name of the molecule and its chemical formula at the
60 top of the screen.
61 -no-titles
63 Do not print the molecule name.
64 -atoms Represent the atoms as shaded spheres of appropriate sizes.
66 This is the default.
67 -no-atoms
69 Do not draw spheres for the atoms: only draw bond lines.
70 -bonds Represent the atomic bonds as solid tubes of appropriate thick‐
72 nesses. This is the default.
73 -no-bonds
75 Do not draw the bonds: instead, make the spheres for the atoms
76 be larger, for a "space-filling" representation of the mole‐
77 cule.
78 -shells Draw transparent electron shells around the atoms. This only
80 works if bonds are also being drawn.
81 -no-shells
83 Do not draw electron shells. This is the default.
84 -shell-alpha
86 When drawing shells, how transparent to make them. Default
87 0.4.
88 -wireframe
90 Draw a wireframe rendition of the molecule: this will consist
91 only of single-pixel lines for the bonds, and text labels where
92 the atoms go. This will be very fast.
93 -timeout seconds
95 When using the built-in data set, change to a new molecule ev‐
96 ery this-many seconds. Default is 20 seconds.
97 -molecule file-or-directory
99 Instead of using the built-in molecules, read one from the
100 given file. This file must be in PDB (Protein Data Base) for‐
101 mat. (Note that it's not uncommon for PDB files to contain
102 only the atoms, with no (or little) information about the
103 atomic bonds.)
104 This can also be a directory, in which case, all of the .pdb
106 files in that directory will be loaded. A new one will be dis‐
107 played at random every few seconds (as per the -timeout op‐
108 tion.)
109 When the molecule is too large (bigger than about 30 angstroms from
111 side to side), the -label option will be automatically turned off, be‐
112 cause otherwise, the labels would overlap and completely obscure the
113 display.
114 When the molecule is around 150 angstroms from side to side, wireframe
116 mode will be turned on (because otherwise it would be too slow.)
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119 DISPLAY to get the default host and display number.
120 XENVIRONMENT
122 to get the name of a resource file that overrides the global
123 resources stored in the RESOURCE_MANAGER property.
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126 X(1), xscreensaver(1)
127 Documentation on the PDB file format:
129 https://web.archive.org/web/20070108054535/https%3A//www.ww‐
131 pdb.org/docs.html
132 https://web.ar‐
133 chive.org/web/19990819134547/https%3A//www.rcsb.org/pdb/docs/for‐
134 mat/pdbguide2.2/guide2.2_frame.html
135 A good source of PDB files:
137 https://www.umass.edu/microbio/rasmol/whereget.htm
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140 Copyright © 2001-2005 by Jamie Zawinski. Permission to use, copy, mod‐
141 ify, distribute, and sell this software and its documentation for any
142 purpose is hereby granted without fee, provided that the above copy‐
143 right notice appear in all copies and that both that copyright notice
144 and this permission notice appear in supporting documentation. No rep‐
145 resentations are made about the suitability of this software for any
146 purpose. It is provided "as is" without express or implied warranty.
147
149 Jamie Zawinski <jwz@jwz.org>
150X Version 11 6.04-1.fc36 (06-Jun-2022) molecule(6x)