Manual tweaks

4 files changed, 46 insertions, 28 deletions

diff --git a/doc/man/check_hkl.1 b/doc/man/check_hkl.1
index d01a8ecc..b6e9430b 100644
--- a/doc/man/check_hkl.1
+++ b/doc/man/check_hkl.1
@@ -12,6 +12,8 @@ check_hkl \- calculate figures of merit for reflection data
 .SH SYNOPSIS
 .PP
 \fBcheck_hkl\fR [\fIoptions\fR] \fB...\fR \fIfile.hkl\fR \fB-p\fR \fIcell.pdb\fR
+.PP
+\fBcheck_hkl --help\fR
 
 .SH DESCRIPTION
 check_hkl calculates figures of merit for reflection data, such as completeness and average signal strengths, in resolution shells.  check_hkl accepts a single reflection list in CrystFEL's format, and you must also provide a unit cell (in a PDB file).
@@ -56,7 +58,7 @@ This page was written by Thomas White.
 .SH REPORTING BUGS
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
-.SH COPYRIGHT
+.SH COPYRIGHT AND DISCLAIMER
 Copyright © 2012 Thomas White <taw@physics.org>
 .P
 check_hkl is part of CrystFEL.
diff --git a/doc/man/compare_hkl.1 b/doc/man/compare_hkl.1
index c7a38ca7..0c7d4ba3 100644
--- a/doc/man/compare_hkl.1
+++ b/doc/man/compare_hkl.1
@@ -11,7 +11,9 @@
 compare_hkl \- compare reflection data
 .SH SYNOPSIS
 .PP
-compare_hkl \fR [\fIoptions\fR] \fB...\fR \fIfile1.hkl\fR \fIfile2.hkl\fR
+\fBcompare_hkl\fR \fR [\fIoptions\fR] \fB...\fR \fIfile1.hkl\fR \fIfile2.hkl\fR
+.PP
+\fBcompare_hkl --help\fR
 
 .SH DESCRIPTION
 compare_hkl compares two sets of reflection data and calculates figures of merit such as R-factors.  Several figures of merit will be displayed on the command line.  Figures of merit can also be calculated in resolution shells.  Reflections will be considered equivalent according to your choice of point group.  The ratios of the reflections can be written to a new file, perhaps to look for systematic effects.
@@ -75,7 +77,7 @@ This page was written by Thomas White.
 .SH REPORTING BUGS
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
-.SH COPYRIGHT
+.SH COPYRIGHT AND DISCLAIMER
 Copyright © 2012 Thomas White <taw@physics.org>
 .P
 compare_hkl is part of CrystFEL.
diff --git a/doc/man/hdfsee.1 b/doc/man/hdfsee.1
index f71b9fa6..8f3779da 100644
--- a/doc/man/hdfsee.1
+++ b/doc/man/hdfsee.1
@@ -12,6 +12,8 @@ hdfsee - HDF5 image viewer
 .SH SYNOPSIS
 .PP
 .B hdfsee \fIimage.h5\fR [\fIoptions\fR] \fB...\fR
+.PP
+\fBhdfsee --help\fR
 
 .SH DESCRIPTION
 hdfsee is a simple image viewer for images stored in HDF5 files.
@@ -86,7 +88,7 @@ This page was written by Thomas White.
 .SH REPORTING BUGS
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
-.SH COPYRIGHT
+.SH COPYRIGHT AND DISCLAIMER
 Copyright © 2012 Thomas White <taw@physics.org>
 .P
 hdfsee is part of CrystFEL.
diff --git a/doc/man/powder_plot.1 b/doc/man/powder_plot.1
index 9a1151fa..1de9a989 100644
--- a/doc/man/powder_plot.1
+++ b/doc/man/powder_plot.1
@@ -59,40 +59,52 @@ intensities.
 
 When taking input from stream, the d-spacing for a particular intensity can be
 generated in a variety of different ways.  You can choose which one with
---data=<type>.  Possible types are:
-
- reflection  : use peak positions from indexed reflections
- hkl         : use the Miller indicies from indexed reflections, combined
-                 with a unit cell from PDB file provided with -p.
- d           : use the 1/d values in the stream for indexed reflections,
-                 which were calculated at the time of indexing using the
-                 unit cell for the individual crystal.  The individual
-                 unit cell should be close to the actual cell, meaning
-                 that this option should give a result close to "hkl".
- peaks       : use peak positions from peak search
- h5          : use all pixels in the HDF5 file, excluding bad regions
-
-The default is
-.BR --data=d .
+\fB--data=\fR\fItype\fR.  Possibilities for \fItype\fR are:
+.RS
+.IP \fBreflection\fR
+.PD
+Use peak positions from indexed reflections
+.IP \fBhkl\fR
+.PD
+Use the Miller indicies from indexed reflections, combined with a unit cell from PDB file provided with -p.
+.IP \fBd\fR
+.PD
+Use the 1/d values in the stream for indexed reflections, which were calculated at the time of indexing using the unit cell for the individual crystal.  The individual unit cell should be close to the actual cell, meaning that this option should give a result close to "hkl".
+.IP \fBpeaks\fR
+.PD
+Use peak positions from peak search
+.IP \fBh5\fR
+.PD
+Use all pixels in the HDF5 file, excluding bad regions
+.RE
+.PP
+The default is \fB--data=d\fR.
 
 
 .SH HISTOGRAM OPTIONS
 
 You can set the mininum and maximum 1/d values, in units of inverse meters,
-with the options
-.B --min=<n>
-and
-.B --max=<n> .
-When taking input from peak positions, The default behaviour is to use the entire detector extent from the geometry description file, which you  with the -g flag.
+with the options \fB-min=\fR\fIn\fR and \fB--max=\fR\fIn\fR.
+When taking input from peak positions, The default behaviour is to use the entire detector extent from the geometry description file, which you  with the \fB-g\fR flag.
 
 You can also adjust the number of histogram bins with the option --bins=<n>,
 where n is an integer.
 
 Scaling can be set to produce linearly, quadratically or cubically spaced 1/d
-values using --spacing=<type>.  Possible types of spacing are:
- linear      : linear (default)
- wilson      : even spacing in Wilson plots (quadratic)
- volume      : constant volume (cubic)
+values using \fB--spacing=\fR\fItype\fR.  Possibilities for \fItype\fR are:
+.RS
+.IP \fBlinear\fR
+.PD
+The resolution shells will have equal widths in terms of 1/d.
+.IP \fBwilson\fR
+.PD
+The resolution shells will be quadratically spaced, giving even spacing in a plot against 1/d^2 (a Wilson plot).
+.IP \fBvolume\fR
+.PD
+The resolution shells will all have equal volumes in reciprocal space.
+.RE
+.PP
+The default is \fB--spacing=linear\fR.
 
 .SH OPTIONS FOR MORE CONTROL