Manual page updates

5 files changed, 14 insertions, 13 deletions

diff --git a/doc/man/cell_tool.1 b/doc/man/cell_tool.1
index 08f22d68..d5ce57af 100644
--- a/doc/man/cell_tool.1
+++ b/doc/man/cell_tool.1
@@ -76,11 +76,11 @@ $ cell_tool --find-ambi 1JB0.pdb -y 6
 .nf
 [...]
 Observed symmetry operations:
-              1 : hkl         -h-k,k,-l   -h-k,h,l    -h,-k,l     -h,h+k,-l
+       Observed : hkl         -h-k,k,-l   -h-k,h,l    -h,-k,l     -h,h+k,-l
                   -k,-h,-l    -k,h+k,l    k,-h-k,l    k,h,-l       h,-h-k,-l
                   h+k,-h,l    h+k,-k,-l
 Ambiguity operations:
-         1 -> 6 : hkl         -h-k,k,-l
+  Observed -> 6 : -h-k,k,-l
 .fi
 
 There are 12 reflections which cannot be distinguished between by the lattice alone, but only 6 of those are true symmetry equivalents according to the structure.  The transformation describing the indexing ambiguity as follows: "A reflection hkl will be confused with one with indices -h-k,k,-l".  Had the point group of the crystals been '622', there would have been no indexing ambiguity (try it!).
@@ -97,10 +97,10 @@ Observed symmetry operations:
               1 : hkl        -h,-k,l    -h,k,-l    -k,-h,-l   -k,h,l
                   k,-h,l     k,h,-l     h,-k,-l
 Ambiguity operations:
-       1 -> 422 : hkl
+Observed -> 422 :
 .fi
 
-All of the apparently equivalent reflections are true symmetry equivalents according to point group 422, so there is no indexing ambiguity.  The only operation produced by left coset decomposition is the identity operation.
+All of the apparently equivalent reflections are true symmetry equivalents according to point group 422, so there is no indexing ambiguity.  No operations are produced by the left coset decomposition.
 
 .PP
 \fBExample 3: "Accidental" ambiguity in myoglobin\fR
@@ -117,9 +117,9 @@ $ cell_tool --find-ambi 3VAU.pdb -y 2_uab
  3.51  2.84  6.33 nm     90.00 106.84  90.00 deg
 [...]
 Observed symmetry operations:
-              1 : hkl         -h,-k,h+l   -h,k,-l     h,-k,-h-l
+       Observed : hkl         -h,-k,h+l   -h,k,-l     h,-k,-h-l
 Ambiguity operations:
-         1 -> 2 : hkl         -h,-k,h+l
+  Observed -> 2 : -h,-k,h+l
 .fi
 
 The transformations '-h,-k,h+l' and 'h,-k,-h-l', which correspond to indexing "diagonally", produce cells which look very similar to the original cell - a difference of only 0.4A and 1.34 degrees.  These two transformations are themselves related by a twofold rotation, which is a true symmetry of this crystal structure.  There is therefore only one ambiguity transformation.  The transformation is strange because it isn't one of the symmetries displayed by a monoclinic lattice in general.  This ambiguity has arisen because of of the particular unit cell parameters for this structure.
diff --git a/doc/man/crystfel.7 b/doc/man/crystfel.7
index f56fa22d..2aad48c5 100644
--- a/doc/man/crystfel.7
+++ b/doc/man/crystfel.7
@@ -45,6 +45,9 @@ A tool for resolving indexing ambiguities.
 .IP \fBget_hkl\fR
 A tool for manipulating reflection lists, such as performing symmetry expansion.
 
+.IP \fBcell_tool\fR
+A tool for manipulating unit cell files, such as applying transformations.
+
 .IP \fBcell_explorer\fR
 A tool for examining the distributions of unit cell parameters.
 
@@ -167,6 +170,7 @@ You should have received a copy of the GNU General Public License along with Cry
 .BR render_hkl (1),
 .BR hdfsee (1),
 .BR get_hkl (1),
+.BR cell_tool (1),
 .BR geoptimiser (1),
 .BR whirligig (1),
 .BR list_events (1),
diff --git a/doc/man/geoptimiser.1 b/doc/man/geoptimiser.1
index a176de6b..3c25b7b3 100644
--- a/doc/man/geoptimiser.1
+++ b/doc/man/geoptimiser.1
@@ -27,10 +27,7 @@ For a complete description of the optimization algorithm, see the following pape
 O. Yefanov, V. Mariani, C. Gati, T. A. White, H. N. Chapman, and A. Barty. "Accurate determination of segmented X-ray detector geometry". Optics Express 23 (2015) 28459. doi:10.1364/OE.23.028459.
 
 .PP
-For minimal basic use, you need to provide a stream file with diffraction patterns, a geometry file to optimize, a filename for the output optimized geometry, and the name of two rigid group collections defined in the geometry file: one describing which panels in the detector are physically connected (and hence whose geometry should be optimized as if they were a single panel), and one to describe which panels are attached to the same underlying support (whose position and orientation are likely to be correlated).
-
-.PP
-If you leave out the \fB-g\fR option, the geometry file from the stream's audit information will be used.  This is usually what you want.
+For minimal basic use, you need to provide a stream file with diffraction patterns, a filename for the output optimized geometry, and the name of two rigid group collections defined in the geometry file: one describing which panels in the detector are physically connected (and hence whose geometry should be optimized as if they were a single panel), and one to describe which panels are attached to the same underlying support (whose position and orientation are likely to be correlated).
 
 .PP
 See \fBman crystfel_geometry\fR for information on how to create a file describing the detector geometry, and guidelines to define the required rigid groups and rigid groups collections.
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 270a4cd3..41e34aa7 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -469,9 +469,9 @@ These set low-level parameters for the PinkIndexer indexing algorithm.
 .IP
 \fB--pinkIndexer-multi\fR Use pinkIndexers own multi indexing. Should be combined with the --no-multi flag.
 .IP
-\fB--pinkIndexer-thread-count\fR sets the thread count for internal parallelization. Default is 1. Very useful for small datasets (e.g. for screening). Internal parallelization does not significantly increase the amount of RAM needed, whereas CrystFELs parallelization does. For HPCs typically a mixture of both parallelizations leads to best results.
+\fB--pinkIndexer-thread-count\fR sets the thread count for internal parallelization. Default is 1. Very useful for small datasets (e.g. for screening). Internal parallelization does not significantly increase the amount of RAM needed, whereas CrystFEL's parallelization does. For HPCs typically a mixture of both parallelizations leads to best results.
 .IP
-\fB--pinkIndexer-no-check-indexed\fR Leave the check whether a pattern is indexed completely to CrystFEL. Useful for monochromatic (since CrystFELs prediction model is smarter than the one of pinkIndexer) or in combnation with --no-check-peaks for geometry optimization. This flag is meant to eventually disappear, when the full pink pipeline is implemented.
+\fB--pinkIndexer-no-check-indexed\fR Leave the check whether a pattern is indexed completely to CrystFEL. Useful for monochromatic (since CrystFEL's prediction model is smarter than the one of pinkIndexer) or in combnation with --no-check-peaks for geometry optimization. This flag is meant to eventually disappear, when the full pink pipeline is implemented.
 .IP
 \fB--pinkIndexer-override-photon-energy=\fIn\fR Overrides the bandwidth in (delta energy)/(mean energy) to use for indexing (which usually is difined in the geometry file). Should be used together with \fB--pinkIndexer-override-bandwidth=\fIn\fR
 .IP
diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index 4f5bd6dd..515f66d7 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -178,7 +178,7 @@ If you prefer, you can specify the ambiguity operator by specifying the apparent
 .PD 0
 .IP \fB--force-bandwidth=\fIbw\fR
 .IP \fB--force-radius=\fIR\fR
-.IP \fB--force-lambda=\fIR\fR
+.IP \fB--force-lambda=\fIl\fR
 .PD
 Set the X-ray bandwidth, initial profile radius or wavelength for all crystals before proceeding, overriding the values from the stream.  Bandwidth is given as a fraction, i.e. \fB--force-bandwidth=0.0013\fR means 0.13 percent (approximate FWHM).  Radius is given in nm^-1.  Wavelength is given in Angstroms.