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] [-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]
14

DESCRIPTION

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.
19

OPTIONS

21       molecule accepts the following options:
22
23       -window Draw on a newly-created window.  This is the default.
24
25       -root   Draw on the root window.
26
27       -install
28               Install a private colormap for the window.
29
30       -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
35       -fps    Display the current frame rate, CPU load, and polygon count.
36
37       -verbose
38               Print debugging info on stderr about files being loaded, etc.
39
40       -wander Move the molecules around the screen.
41
42       -no-wander
43               Keep the molecule centered on the screen.  This is the default.
44
45       -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
50       -no-spin
51               Don't spin it at all: the same as -spin "".
52
53       -labels Draw labels on the atoms (or the spot  where  the  atoms  would
54               be.)  This is the default.
55
56       -no-labels
57               Do not draw labels on the atoms.
58
59       -titles Print  the name of the molecule and its chemical formula at the
60               top of the screen.
61
62       -no-titles
63               Do not print the molecule name.
64
65       -atoms  Represent the atoms as shaded  spheres  of  appropriate  sizes.
66               This is the default.
67
68       -no-atoms
69               Do not draw spheres for the atoms: only draw bond lines.
70
71       -bonds  Represent the atomic bonds as solid tubes of appropriate thick‐
72               nesses.  This is the default.
73
74       -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
79       -shells Draw transparent electron shells around the atoms.   This  only
80               works if bonds are also being drawn.
81
82       -no-shells
83               Do not draw electron shells.  This is the default.
84
85       -shell-alpha
86               When  drawing  shells,  how  transparent to make them.  Default
87               0.4.
88
89       -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
94       -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
98       -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
105               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
110       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
115       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.)
117

ENVIRONMENT

119       DISPLAY to get the default host and display number.
120
121       XENVIRONMENT
122               to get the name of a resource file that  overrides  the  global
123               resources stored in the RESOURCE_MANAGER property.
124

SEE ALSO

126       X(1), xscreensaver(1)
127
128       Documentation on the PDB file format:
129
130       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
136       A good source of PDB files:
137       https://www.umass.edu/microbio/rasmol/whereget.htm
138
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

AUTHOR

149       Jamie Zawinski <jwz@jwz.org>
150
151
152
153X Version 11               6.04-1.fc36 (06-Jun-2022)              molecule(6x)
Impressum