Update docs

1 files changed, 42 insertions, 13 deletions

diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index 63fb062c..32bd433c 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -28,9 +28,11 @@ of diffraction for each pattern (crystal orientation, unit cell parameters,
 X-ray bandwidth and so on) and attempts to optimise the geometrical parameters
 to make the fully integrated intensities calculated using the model agree as
 closely as possible between the many patterns.
-.PP
-This program is \fIexperimental\fR in this version of CrystFEL.  It is not yet
-considered ready for processing experimental data.
+
+See USAGE CASES below for examples of commands to merge reflections in different
+ways, for example with and without partiality or scaling.
+
+In addition to the output reflection list, \fBpartialator\fR will write a file called partialator.params which contains the scaling factors determined for each crystal.  After each iteration, a file will be written called pgraph-iter\fIn\fR.dat which contains the observed and calculated partialities for a randomly chosen set of "free" reflections which were not included in the refinement.
 
 .SH OPTIONS
 .PD 0
@@ -43,8 +45,7 @@ Give the name of the input stream.
 .IP "\fB-o\fR \fIfilename\fR"
 .IP \fB--output=\fR\fIfilename\fR
 .PD
-Give the name of the output file.  The default is
-\fB--output=partialator.hkl\fR.
+Give the name of the output file.  The default is \fB--output=partialator.hkl\fR.
 
 .PD 0
 .IP "\fB-y\fR \fIpointgroup\fR"
@@ -89,6 +90,11 @@ Include reflections only if their peak values were less than \fIn\fR.  That mean
 .PD
 Include a reflection in the output only if it appears at least least \fIn\fR times.  The default is \fB--min-measurements=2\fR.
 
+.PD 0
+.IP \fB--push-res=\fIn\fR
+.PD
+Merge reflections which are up to \fIn\fR nm^-1 higher than the apparent resolution limit of each individual crystal.  \fIn\fR can be negative to merge \fIlower\fR than the apparent resolution limit.  The default is \fB--rescut=0\fR - note that this is different to the default behaviour of \fBprocess_hkl\fR.
+
 .SH PARTIALITY MODELS
 
 The available partiality models are:
@@ -98,7 +104,7 @@ The available partiality models are:
 The volume of intersection between a sphere centered on each reciprocal lattice
 point and the part of reciprocal space excited by the Ewald sphere taking into
 account the finite bandwidth and convergence angle.  A "source coverage factor"
-will be included to take into account the spectral brightness of the effective
+is included to take into account the spectral brightness of the effective
 source for the reflection.
 
 This model is similar to that described in Acta Cryst. D69 (2013) p1231-1240,
@@ -117,13 +123,37 @@ radius (determined by indexamajig) divided by 2.6.
 .PD
 Fix all partialities at 1.
 
+.SH USAGE CASES
 
-.SH BUGS
-This program is \fIexperimental\fR in this version of CrystFEL.  It is not
-yet considered ready for processing experimental data.  Your pet kitten may
-explode if you attempt to solve a structure using intensities calculated by this
-program.
+.IP "Merging without scaling, partialities or post-refinement:"
+.PD
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=unity --iterations=0\fR
 
+.IP "Merging without partialities or post-refinement, but with scaling:"
+.PD
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=unity --iterations=1\fR
+.IP
+(Use a higher number of iterations to increase the accuracy of scaling, but at a cost of more CPU time and possibly more rejected crystals)
+
+.IP "Merging with partialities, but without post-refinement and without scaling:"
+.PD
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=0\fR
+
+.IP "Merging with partialities, post-refinement and scaling:"
+.PD
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=1\fR
+.IP
+(Use a higher number of iterations to increase the accuracy of scaling and post-refinement, but at a cost of more CPU time and possibly more rejected crystals)
+
+.IP "Merging with partialities and post-refinement, but without scaling:"
+.PD
+This would be a strange thing to want to do, however:
+.IP
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=1 --no-scale\fR
+.IP
+(Use a higher number of iterations to increase the accuracy of post-refinement, but at a cost of more CPU time and possibly more rejected crystals)
+.PP
+\fBscguassian\fR could be substituted for \fBscsphere\fR in the above examples to use the Gaussian partiality model instead of the spherical one.
 
 .SH AUTHOR
 This page was written by Thomas White.
@@ -146,5 +176,4 @@ You should have received a copy of the GNU General Public License along with Cry
 .BR crystfel (7),
 .BR indexamajig (1),
 .BR process_hkl (1),
-.BR partial_sim (1),
-.BR crystfel_geometry (5).
+.BR partial_sim (1)