Introduce CrystFEL unit cell files

8 files changed, 40 insertions, 15 deletions

diff --git a/doc/examples/cell-example.cell b/doc/examples/cell-example.cell
new file mode 100644
index 00000000..ac236214
--- /dev/null
+++ b/doc/examples/cell-example.cell
@@ -0,0 +1,12 @@
+CrystFEL unit cell file version 1.0
+
+lattice_type = cubic
+centering = I
+
+a = 66.2 A
+b = 66.2 A
+c = 66.2 A
+
+al = 90.0 deg
+be = 90.0 deg
+ga = 90.0 deg
diff --git a/doc/man/check_hkl.1 b/doc/man/check_hkl.1
index 7e21dd10..4853a482 100644
--- a/doc/man/check_hkl.1
+++ b/doc/man/check_hkl.1
@@ -20,10 +20,11 @@ check_hkl calculates figures of merit for reflection data, such as completeness
 
 .SH OPTIONS
 .PD 0
+.IP "\fB-p\fR \fIunitcell.cell\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.
+Specify the name of the file containing unit cell information, in PDB or CrystFEL format.
 
 .PD 0
 .IP "\fB-y\fR \fIpointgroup\fR"
diff --git a/doc/man/compare_hkl.1 b/doc/man/compare_hkl.1
index b2374b73..0ae6a890 100644
--- a/doc/man/compare_hkl.1
+++ b/doc/man/compare_hkl.1
@@ -26,10 +26,11 @@ compare_hkl compares two sets of reflection data and calculates figures of merit
 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.cell\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.
+Specify the name of the file containing unit cell information, in PDB or CrystFEL format.
 
 .PD 0
 .IP \fB--fom=\fR\fIFoM\fR
diff --git a/doc/man/get_hkl.1 b/doc/man/get_hkl.1
index 92b8ce37..94c73579 100644
--- a/doc/man/get_hkl.1
+++ b/doc/man/get_hkl.1
@@ -77,10 +77,11 @@ In the first form, reflections with d (=lamba/2*sin(theta)) < \fIn\fR will be re
 In the second form, anisotropic truncation will be performed with separate resolution limits \fIn1\fR, \fIn2\fR and \fIn3\fR along a*, b* and c* respectively.  You must also specify \fB-p\fR or \fB--pdb\fR.
 
 .PD 0
+.IP "\fB-p\fR \fIunitcell.cell\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.
+Specify the name of the file containing unit cell information, in PDB or CrystFEL format.
 
 .SH AUTHOR
 This page was written by Thomas White.
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 4b90d762..71f836c6 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -22,7 +22,7 @@ indexamajig \- bulk indexing and data reduction program
 
 \fBindexamajig\fR takes a list of diffraction snapshots from crystals in random orientations and attempts to find peaks, index and integrate each one.  The input is a list of diffraction image files in HDF5 format and some auxiliary files and parameters.  The output is a long text file ('stream') containing the results from each image in turn.
 
-For minimal basic use, you need to provide the list of diffraction patterns, the method which will be used to index, a file describing the geometry of the detector, and a PDB file which contains the unit cell which will be used for the indexing.  Here is what the minimal use might look like on the command line:
+For minimal basic use, you need to provide the list of diffraction patterns, the method which will be used to index, a file describing the geometry of the detector, and a file which contains the unit cell which will be used for the indexing.  Here is what the minimal use might look like on the command line:
 
 .IP \fBindexamajig\fR
 .PD
@@ -57,7 +57,7 @@ To use this option, 'dirax' must be in your shell's search path.  If you see the
 
 .IP \fBmosflm\fR
 .PD
-As \fBdirax\fR, but invoke MOSFLM instead.  If you provide a PDB file (with \fB-p\fR), the lattice type and centering information will be passed to MOSFLM, which will then return solutions which match.  Note that the lattice parameter information will \fBnot\fR be given to MOSFLM, because it has no way to make use of it.
+As \fBdirax\fR, but invoke MOSFLM instead.  If you provide a unit cell (with \fB-p\fR), the lattice type and centering information will be passed to MOSFLM, which will then return solutions which match.  Note that the lattice parameter information will \fBnot\fR be given to MOSFLM, because it has no way to make use of it.
 .sp
 To use this option, 'ipmosflm' must be in your shell's search path.  If you see the MOSFLM version and copyright information when you run \fBipmosflm\fR on the command line, things are set up correctly.
 
@@ -96,7 +96,7 @@ Do not check that the cell accounts for any of the peaks as described in \fBdira
 
 .IP \fB-nolatt\fR
 .PD
-Do not use the lattice type information from the PDB file to help guide the indexing.  Use with \fBmosflm\fR, which is the only indexing method which can optionally take advantage of this information.  This is the default behaviour for \fBdirax\fR.  This option makes no sense for \fBreax\fR, which is intrinsically based on using known lattice information.
+Do not use the lattice type information to help guide the indexing.  Use with \fBmosflm\fR, which is the only indexing method which can optionally take advantage of this information.  This is the default behaviour for \fBdirax\fR.  This option makes no sense for \fBreax\fR, which is intrinsically based on using known lattice information.
 
 .IP \fB-latt\fR
 .PD
@@ -198,10 +198,11 @@ Read the detector geometry description from \fIfilename\fR.  See \fBman crystfel
 Read the beam description from \fIfilename\fR.  See \fBman crystfel_geometry\fR for more information.
 
 .PD 0
-.IP "\fB-p\fR \fIfilename\fR"
-.IP \fB--pdb=\fR\fIfilename\fR
+.IP "\fB-p\fR \fIunitcell.cell\fR"
+.IP "\fB-p\fR \fIunitcell.pdb\fR"
+.IP \fB--pdb=\fR\fIunitcell.pdb\fR
 .PD
-Read the unit cell for comparison from the CRYST1 line of the PDB file called \fIfilename\fR.
+Specify the name of the file containing unit cell information, in PDB or CrystFEL format.
 
 .PD 0
 .IP "\fB-e\fR \fIpath\fR"
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1
index 2af472e9..0c30ba73 100644
--- a/doc/man/partial_sim.1
+++ b/doc/man/partial_sim.1
@@ -25,7 +25,7 @@ partial_sim \- calculate partial reflections
 partial_sim calculates the intensities of idealised partial reflections from crystals in random orientations, which is useful for testing the convergence of Monte Carlo integration or scaling/post-refinement techniques.
 
 .P
-You need to provide a CrystFEL geometry file (with \fB--geometry=\fR\fImy.geom\fR or \fB-g\fR \fImy.geom\fR), a beam description file (with \fB--beam=\fR\fImy.beam\fR or \fB-b\fR \fImy.beam\fR), a PDB file containing at least a CRYST1 line specifying the unit cell to use for the simulation (with \fB--pdb=\fR\fImy.pdb\fR or \fB-p\fR \fImy.pdb\fR), and an output filename with \fB--output=\fR\fImy.stream\fR or \fB-o\fR \fImy.stream\fR.
+You need to provide a CrystFEL geometry file (with \fB--geometry=\fR\fImy.geom\fR or \fB-g\fR \fImy.geom\fR), a beam description file (with \fB--beam=\fR\fImy.beam\fR or \fB-b\fR \fImy.beam\fR), a file containing the unit cell to use for the simulation (with \fB--pdb=\fR\fImy.pdb\fR or \fB-p\fR \fImy.pdb\fR), and an output filename with \fB--output=\fR\fImy.stream\fR or \fB-o\fR \fImy.stream\fR.
 
 For each randomly generated orientation, partial_sim calculates which reflections would appear on the detector with the specified beam parameters.  It calculates the partiality for each reflection and multiplies it by the fully integrated intensity to produce a partial intensity.  The fully integrated intensities can be taken from a file you provide (see below), otherwise they will be randomly generated (by taking the absolute value of a Gaussian random number, mean zero and standard deviation 1000).  All the partial intensities for the orientation are multiplied by an overall scaling factor, which is randomly generated with a Gaussian distribution with mean 1 and standard deviation 0.3.  The partial intensities are written to the output stream, and the process repeated for as many different orientations as you ask for (see below, default: 2).
 
@@ -48,6 +48,13 @@ Take the fully integrated reflection intensities from \fIfile.hkl\fR, instead of
 Specify the number of different orientations to simulate.  Default: 2.
 
 .PD 0
+.IP "\fB-p\fR \fIunitcell.cell\fR"
+.IP "\fB-p\fR \fIunitcell.pdb\fR"
+.IP \fB--pdb=\fR\fIunitcell.pdb\fR
+.PD
+Specify the name of the file containing unit cell information, in PDB or CrystFEL format.
+
+.PD 0
 .B
 .IP "-r \fIrandom.hkl\fR"
 .B
diff --git a/doc/man/pattern_sim.1 b/doc/man/pattern_sim.1
index e71413db..1c3a3b41 100644
--- a/doc/man/pattern_sim.1
+++ b/doc/man/pattern_sim.1
@@ -25,17 +25,18 @@ pattern_sim simulates diffraction patterns from small crystals probed with femto
 
 pattern_sim -g mydetector.geom -b my.beam -p my.pdb -r -i myintensities.hkl
 
-The unit cell geometry will be taken from the CRYST1 line in the PDB file you provide, and the intensities of the reflections will be interpolated from the reflection list file you provide.  The reflection list format is the same as that output by process_hkl and handled by get_hkl.  You also need beam and geometry description files (-b and -g respectively).  See `man crystfel_geometry' for details of how to create a geometry file.  Examples of both files can be found in the installation directory, which is normally /usr/local/share/doc/crystfel.
+The unit cell geometry will be taken from the unit cell file you provide, and the intensities of the reflections will be interpolated from the reflection list file you provide.  The reflection list format is the same as that output by process_hkl and handled by get_hkl.  You also need beam and geometry description files (-b and -g respectively).  See `man crystfel_geometry' for details of how to create a geometry file.  Examples of both files can be found in the installation directory, which is normally /usr/local/share/doc/crystfel.
 
 The result will be written to an HDF5 file in the current directory with the name `sim.h5'.
 
 .SH OPTIONS
 
 .PD 0
+.IP "\fB-p\fR \fIunitcell.cell\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.
+Specify the name of the file containing unit cell information, in PDB or CrystFEL format.
 
 .PD 0
 .IP \fB--gpu\fR
diff --git a/doc/man/render_hkl.1 b/doc/man/render_hkl.1
index ff55e9f0..bd8b40c8 100644
--- a/doc/man/render_hkl.1
+++ b/doc/man/render_hkl.1
@@ -46,10 +46,11 @@ hence represents the Laue zone number.
 Write the output (in PDF format) to \fIfilename\fR.  Default: \fB--output=za.pdf\fR.
 
 .PD 0
-.IP "\fB-p\fR \fIfilename\fR"
-.IP \fB--pdb=\fR\fIfilenamefR
+.IP "\fB-p\fR \fIunitcell.cell\fR"
+.IP "\fB-p\fR \fIunitcell.pdb\fR"
+.IP \fB--pdb=\fR\fIunitcell.pdb\fR
 .PD
-Get the unit cell parameters from the CRYST1 line contained in \fIfilename\fR.
+Specify the name of the file containing unit cell information, in PDB or CrystFEL format.
 
 .PD 0
 .IP \fB--boost=\fR\fIn\fR