-.de EX \"Begin example
-.ne 5
-.if n .sp 1
-.if t .sp .5
-.nf
-.in +.5i
-..
-.de EE
-.fi
-.in -.5i
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.TH XScreenSaver 1 "13-Mar-01" "X Version 11"
.SH NAME
-molecule - draws 3D moleclear structures
+molecule - draws 3D molecular structures
.SH SYNOPSIS
-.B gltext
+.B molecule
[\-display \fIhost:display.screen\fP] [\-window] [\-root]
-[\-visual \fIvisual\fP] [\-delay \fImicroseconds\fP] [\-fps]
+[\-visual \fIvisual\fP] [\-delay \fImicroseconds\fP]
[\-wander] [\-no-wander]
[\-spin \fIaxes\fP]
[\-no-spin]
-[\-wire]
[\-timeout \fIseconds\fP]
[\-labels] [\-no-labels]
[\-titles] [\-no-titles]
[\-atoms] [\-no-atoms]
[\-bonds] [\-no-bonds]
-[\-molecule \fIfilename\fP]
+[\-shells] [\-no-shells]
+[\-molecule \fIfile-or-directory\fP]
+[\-verbose]
+[\-wireframe]
+[\-fps]
.SH DESCRIPTION
The \fImolecule\fP program draws several different representations of
molecules. Some common molecules are built in, and it can read PDB
or the id number (decimal or hex) of a specific visual.
.TP 8
.B \-fps
-Display a running tally of how many frames per second are being rendered.
-In conjunction with \fB\-delay 0\fP, this can be a useful benchmark of
-your GL performance.
+Display the current frame rate, CPU load, and polygon count.
+.TP 8
+.B \-verbose
+Print debugging info on stderr about files being loaded, etc.
.TP 8
.B \-wander
Move the molecules around the screen.
Do not draw the bonds: instead, make the spheres for the atoms be
larger, for a "space-filling" representation of the molecule.
.TP 8
-.B \-wire
+.B \-shells
+Draw transparent electron shells around the atoms. This only works
+if bonds are also being drawn.
+.TP 8
+.B \-no\-shells
+Do not draw electron shells. This is the default.
+.TP 8
+.B \-shell\-alpha
+When drawing shells, how transparent to make them. Default 0.4.
+.TP 8
+.B \-wireframe
Draw a wireframe rendition of the molecule: this will consist only of
single-pixel lines for the bonds, and text labels where the atoms go.
This will be very fast.
When using the built-in data set, change to a new molecule every
this-many seconds. Default is 20 seconds.
.TP 8
-.B \-molecule \fIfilename\fP
+.B \-molecule \fIfile-or-directory\fP
Instead of using the built-in molecules, read one from the given file.
This file must be in PDB (Protein Data Base) format. (Note that it's
not uncommon for PDB files to contain only the atoms, with no (or
little) information about the atomic bonds.)
+
+This can also be a directory, in which case, all of the .pdb files in
+that directory will be loaded. A new one will be displayed at random
+every few seconds (as per the \fI\-timeout\fP option.)
.PP
When the molecule is too large (bigger than about 30 angstroms from
side to side), the \fI\-label\fP option will be automatically turned
.BR xscreensaver (1)
.PP
Documentation on the PDB file format:
-.EX
-http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
-.EE
+
+ http://www.wwpdb.org/docs.html
+ http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
+
A good source of PDB files:
-.EX
-http://www.sci.ouc.bc.ca/chem/molecule/molecule.html
-.EE
+
+ http://www.umass.edu/microbio/rasmol/whereget.htm
+ http://www.wwpdb.org/docs.html
.SH COPYRIGHT
-Copyright \(co 2001 by Jamie Zawinski.
+Copyright \(co 2001-2005 by Jamie Zawinski.
Permission to use, copy, modify, distribute, and sell this software and
its documentation for any purpose is hereby granted without fee,
provided that the above copyright notice appear in all copies and that
projects / xscreensaver / blobdiff