X-Git-Url: http://git.hungrycats.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=hacks%2Fglx%2Fmolecule.man;h=f16fd6b714ece11f4ed8f88c8a5c3a410df0823d;hb=447db08c956099b3b183886729108bf5b364c4b8;hp=1b92b6b355c3eb335be4b0ed0916741eb9a3bb90;hpb=e4fa2ac140f7bc56571373a7b7eb585fa4500e38;p=xscreensaver

diff --git a/hacks/glx/molecule.man b/hacks/glx/molecule.man
index 1b92b6b3..f16fd6b7 100644
--- a/hacks/glx/molecule.man
+++ b/hacks/glx/molecule.man
@@ -1,16 +1,3 @@
-.de EX		\"Begin example
-.ne 5
-.if n .sp 1
-.if t .sp .5
-.nf
-.in +.5i
-..
-.de EE
-.fi
-.in -.5i
-.if n .sp 1
-.if t .sp .5
-..
 .TH XScreenSaver 1 "13-Mar-01" "X Version 11"
 .SH NAME
 molecule - draws 3D moleclear structures
@@ -22,12 +9,14 @@ molecule - draws 3D moleclear structures
 [\-spin \fIaxes\fP]
 [\-no-spin]
 [\-wire]
+[\-verbose]
 [\-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]
 .SH DESCRIPTION
 The \fImolecule\fP program draws several different representations of
 molecules.  Some common molecules are built in, and it can read PDB
@@ -54,6 +43,9 @@ 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.
 .TP 8
+.B \-verbose
+Print debugging info on stderr about files being loaded, etc.
+.TP 8
 .B \-wander
 Move the molecules around the screen.
 .TP 8
@@ -98,6 +90,16 @@ This is the default.
 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 \-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 \-wire
 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.
@@ -138,15 +140,14 @@ stored in the RESOURCE_MANAGER property.
 .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.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.sci.ouc.bc.ca/chem/molecule/molecule.html
 .SH COPYRIGHT
-Copyright \(co 2001, 2004 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