Fixes for manual pages from lintian

6 files changed, 23 insertions, 23 deletions

diff --git a/doc/man/check_hkl.1 b/doc/man/check_hkl.1
index 4c411d7d..7e21dd10 100644
--- a/doc/man/check_hkl.1
+++ b/doc/man/check_hkl.1
@@ -1,7 +1,7 @@
 .\"
 .\" check_hkl man page
 .\"
-.\" Copyright © 2012 Thomas White <taw@physics.org>
+.\" Copyright © 2012-2014 Thomas White <taw@physics.org>
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
 .\"
@@ -20,38 +20,38 @@ check_hkl calculates figures of merit for reflection data, such as completeness
 
 .SH OPTIONS
 .PD 0
-.IP \fB-p\fR \fIunitcell.pdb\fR
+.IP "\fB-p\fR \fIunitcell.pdb\fR"
 .IP \fB--pdb=\fR\fIunitcell.pdb\fR
 .PD
 Specify the name of the PDB file containing at least a CRYST1 line describing the unit cell.
 
 .PD 0
-.IP \fB-y\fR \fpointgroup\fR
+.IP "\fB-y\fR \fIpointgroup\fR"
 .IP \fB--symmetry=\fR\fIpointgroup\fR
 .PD
 Specify the symmetry of the reflections.
 
 .PD 0
-.IP \fB--sigma-cutoff=\fR\fIn\fR
+.IP "\fB--sigma-cutoff=\fR\fIn\fR"
 .PD
 Discard reflections with I/sigma(I) < \fIn\fR.  Default: -infinity (no cutoff).
 
 .PD 0
-.IP \fB--rmin=\fR\fI1/d\fR
+.IP "\fB--rmin=\fR\fI1/d\fR"
 .PD
 Low resolution cutoff, as 1/d in m^-1.  Use this or \fB--lowres\fR, but not both.
 
 .PD 0
-.IP \fB--lowres=\fR\fId\fR
+.IP "\fB--lowres=\fR\fId\fR"
 Low resolution cutoff in Angstroms.  Use this or \fB--rmin\fR, but not both.
 
 .PD 0
-.IP \fB--rmax=\fR\fI1/d\fR
+.IP "\fB--rmax=\fR\fI1/d\fR"
 .PD
 High resolution cutoff, as 1/d in m^-1.  Use this or \fB--highres\fR, but not both.
 
 .PD 0
-.IP \fB--highres=\fR\fId\fR
+.IP "\fB--highres=\fR\fId\fR"
 High resolution cutoff in Angstroms.  Use this or \fB--rmax\fR, but not both.
 
 .PD 0
@@ -91,7 +91,7 @@ This page was written by Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 check_hkl, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/compare_hkl.1 b/doc/man/compare_hkl.1
index 1b4cdf4b..560104a5 100644
--- a/doc/man/compare_hkl.1
+++ b/doc/man/compare_hkl.1
@@ -20,13 +20,13 @@ compare_hkl compares two sets of reflection data and calculates figures of merit
 
 .SH OPTIONS
 .PD 0
-.IP \fB-y\fR \fpointgroup\fR
+.IP "\fB-y\fR \fpointgroup\fR"
 .IP \fB--symmetry=\fR\fIpointgroup\fR
 .PD
 Specify the symmetry of the reflections.  The symmetry must be the same for both lists of reflections.  Default: 1 (no symmetry).
 
 .PD 0
-.IP \fB-p\fR \fIunitcell.pdb\fR
+.IP "\fB-p\fR \fIunitcell.pdb\fR"
 .IP \fB--pdb=\fR\fIunitcell.pdb\fR
 .PD
 Specify the name of the PDB file containing at least a CRYST1 line describing the unit cell.
diff --git a/doc/man/crystfel.7 b/doc/man/crystfel.7
index 92669e8b..9910ee18 100644
--- a/doc/man/crystfel.7
+++ b/doc/man/crystfel.7
@@ -47,7 +47,7 @@ A tool for manipulating reflection lists, such as performing symmetry expansion.
 .IP \fBcell_explorer\fR
 A tool for examining the distributions of unit cell parameters.
 
-.IP \fBcompare_hkl\fR and \fBcheck_hkl\fR
+.IP "\fBcompare_hkl\fR and \fBcheck_hkl\fR"
 Tools for calculating figures of merit, such as completeness and R-factors.
 
 .IP \fBpartial_sim\fB
diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5
index f2745a93..6f51c01e 100644
--- a/doc/man/crystfel_geometry.5
+++ b/doc/man/crystfel_geometry.5
@@ -7,8 +7,8 @@
 .\"
 
 .TH CRYSTFEL\_GEOMETRY 5
-
-.SH CRYSTFEL DETECTOR GEOMETRY AND BEAM DESCRIPTION FILES
+.SH NAME
+CRYSTFEL DETECTOR GEOMETRY AND BEAM DESCRIPTION FILES
 
 See below for information about CrystFEL's beam description files.
 
diff --git a/doc/man/hdfsee.1 b/doc/man/hdfsee.1
index da3a51f3..68347264 100644
--- a/doc/man/hdfsee.1
+++ b/doc/man/hdfsee.1
@@ -73,7 +73,7 @@ Show resolution rings on the image at 1 Angstrom intervals.  You must provide bo
 Show rings on the image with the radii specified.  \fIradii\fR can be a comma-deliminated list of several values, for example \fI100,200\fR.  The radii have units of pixels on the detector before bininng.  You must provide a geometry file to use this option.
 
 .PD 0
-.IP \fB-c\fR \fIscale\fR
+.IP "\fB-c\fR \fIscale\fR"
 .IP \fB--colscale=\fR\fIscale\fR
 .PD
 Use \fIscale\fR as the colour scale.  Possible scales are: \fBmono\fR, \fBinvmono\fR and \fBcolour\fR.
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1
index db615dac..b3e5c9a2 100644
--- a/doc/man/partial_sim.1
+++ b/doc/man/partial_sim.1
@@ -44,7 +44,7 @@ for information about CrystFEL geometry description files.
 Take the fully integrated reflection intensities from \fIfile.hkl\fR, instead of generating them randomly.
 
 .B
-.IP \fB-n\fR \fIn\fR
+.IP "\fB-n\fR \fIn\fR"
 Specify the number of different orientations to simulate.  Default: 2.
 
 .PD 0
@@ -59,7 +59,7 @@ If you did not provide your own fully integrated reflection intensities, they wi
 .B
 .IP "\fB-y\fR \fIpointgroup\fR"
 .B
-.IP \fB--symmetry=\fR\fIpointgroup\fR
+.IP "\fB--symmetry=\fR\fIpointgroup\fR"
 .PD
 When combined with with \fB-i\fR, specifies the symmetry of the input reflection list.  Otherwise, specifies the symmetry of the randomly generated intensities.
 
@@ -67,31 +67,31 @@ When combined with with \fB-i\fR, specifies the symmetry of the input reflection
 .B
 .IP "\fB-c\fR \fIval\fR"
 .B
-.IP "\fB--cnoise=\fR\fIval\fR
+.IP "\fB--cnoise=\fR\fIval\fR"
 .PD
 Add random values with a flat distribution to the components of the reciprocal lattice vectors written to the stream, simulating indexing errors.  The maximum value that will be added is +/- \fIval\fR percent.
 
 .PD 0
 .B
-.IP "\fB--pgraph=\fR\fIfilename\fR
+.IP "\fB--pgraph=\fR\fIfilename\fR"
 .PD
 Save a table of values to \fIfilename\fR containing, in resolution shells, the following columns: resolution shell centre in nm^-1, number of reflections in shell, mean partiality, maximum partiality.
 
 .PD 0
 .B
-.IP "\fB--osf-stddev=\fR\fIval\fR
+.IP "\fB--osf-stddev=\fR\fIval\fR"
 .PD
 Set the standard deviation of the distribution of overall scaling factors to \fIval\fR.  The distribution will be cut at zero, i.e. negative or zero scaling factors are not allowed.  The distribution will be Gaussian centered on 1.  The default is \fB--osf-stddev=2.0\fR.
 
 .PD 0
 .B
-.IP "\fB--full-stddev=\fR\fIval\fR
+.IP "\fB--full-stddev=\fR\fIval\fR"
 .PD
 Set the standard deviation of the distribution of randomly generated full intensities to \fIval\fR.  The distribution will be Gaussian, centered on zero, and the absolute value will be taken (i.e. there will be no negative values).  The default is \fB--full-stddev=1000.0\fR.  This option has no effect if you also use \fB-i\fR or \fB--input\fR.
 
 .PD 0
 .B
-.IP "\fB--noise-stddev=\fR\fIval\fR
+.IP "\fB--noise-stddev=\fR\fIval\fR"
 .PD
 Set the standard deviation of the noise added to the partial intensities to \fIval\fR.  The noise will be Gaussian, and the same for all reflections.  The default is \fB--noise-stddev=20.0\fR.
 
@@ -103,7 +103,7 @@ Use \fIn\fR threads for simulation.  Default: 1.
 
 .PD 0
 .B
-.IP "\fB--images=\fR\fIprefix\fR
+.IP "\fB--images=\fR\fIprefix\fR"
 .PD
 For each chunk in the output stream, write an image in HDF5 format to \fIprefix\fR\fB/sim-\fR\fINNN\fR\fB.h5\fR, where \fINNN\fR is the sequence number of the chunk in the output stream.  This option is incompatible with \fB-j\fR.