1molecule(6x)                  XScreenSaver manual                 molecule(6x)
2
3
4

NAME

6       molecule - draws 3D molecular structures
7

SYNOPSIS

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

DESCRIPTION

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.
20

OPTIONS

22       molecule accepts the following options:
23
24       --window
25               Draw on a newly-created window.  This is the default.
26
27       --root  Draw on the root window.
28
29       --window-id number
30               Draw on the specified window.
31
32       --install
33               Install a private colormap for the window.
34
35       --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
40       --fps   Display the current frame rate, CPU load, and polygon count.
41
42       --verbose
43               Print debugging info on stderr about files being loaded, etc.
44
45       --wander
46               Move the molecules around the screen.
47
48       --no-wander
49               Keep the molecule centered on the screen.  This is the default.
50
51       --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
56       --no-spin
57               Don't spin it at all: the same as --spin "".
58
59       --labels
60               Draw  labels  on  the  atoms (or the spot where the atoms would
61               be.)  This is the default.
62
63       --no-labels
64               Do not draw labels on the atoms.
65
66       --titles
67               Print the name of the molecule and its chemical formula at  the
68               top of the screen.
69
70       --no-titles
71               Do not print the molecule name.
72
73       --atoms Represent  the  atoms  as  shaded spheres of appropriate sizes.
74               This is the default.
75
76       --no-atoms
77               Do not draw spheres for the atoms: only draw bond lines.
78
79       --bonds Represent the atomic bonds as solid tubes of appropriate thick‐
80               nesses.  This is the default.
81
82       --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
87       --shells
88               Draw  transparent  electron shells around the atoms.  This only
89               works if bonds are also being drawn.
90
91       --no-shells
92               Do not draw electron shells.  This is the default.
93
94       --shell-alpha
95               When drawing shells, how transparent  to  make  them.   Default
96               0.4.
97
98       --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
103       --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
107       --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
114               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
119       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
124       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.)
126

ENVIRONMENT

128       DISPLAY to get the default host and display number.
129
130       XENVIRONMENT
131               to  get  the  name of a resource file that overrides the global
132               resources stored in the RESOURCE_MANAGER property.
133
134       XSCREENSAVER_WINDOW
135               The window ID to use with --root.
136

SEE ALSO

138       X(1), xscreensaver(1)
139
140       Documentation on the PDB file format:
141
142       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
148       A good source of PDB files:
149       https://www.umass.edu/microbio/rasmol/whereget.htm
150
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

AUTHOR

161       Jamie Zawinski <jwz@jwz.org>
162
163
164
165X Version 11               6.06-1.fc37 (12-Dec-2022)              molecule(6x)
Impressum