diff options
| -rw-r--r-- | doc/man/check_hkl.1 | 6 | ||||
| -rw-r--r-- | doc/man/crystfel.7 | 32 | ||||
| -rw-r--r-- | doc/man/pattern_sim.1 | 106 | ||||
| -rw-r--r-- | tests/symmetry_check.c | 1 |
4 files changed, 139 insertions, 6 deletions
diff --git a/doc/man/check_hkl.1 b/doc/man/check_hkl.1 index df1f857e..39dd97ac 100644 --- a/doc/man/check_hkl.1 +++ b/doc/man/check_hkl.1 @@ -37,12 +37,6 @@ Specify the symmetry of the reflections. Discard reflections with I/sigma(I) < \fIn\fR. Default: -infinity (no cutoff). .PD 0 -.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--rmin=\fR\fI1/d\fR .PD Fix the lower resolution limit for the resolutions shells, as 1/d in m^-1. diff --git a/doc/man/crystfel.7 b/doc/man/crystfel.7 index 3d9b3fb7..711b7552 100644 --- a/doc/man/crystfel.7 +++ b/doc/man/crystfel.7 @@ -81,6 +81,38 @@ H. N. Chapman. "CrystFEL: a software suite for snapshot serial crystallography". Please let us know (see below) about your publication, so we can include it in the list of examples on the CrystFEL website. +.SH SYMMETRY IN CRYSTFEL +Without only a very few exceptions, CrystFEL is not interested in space groups. Instead, it deals with point groups which embody the information about how data should be merged from different crystals. Every space group belongs to exactly one point group, and you can look up the right one in the International Tables or using the symmetry tables accompanying the CrystFEL source (or to be found on the CrystFEL website in the Theory section). + +A limitation of symmetry in the current version of CrystFEL is that it can only accept point groups in standard settings. That means that the highest-order rotation axis must always be parallel to c*, monoclinic unit cells should have \fIc\fR as the unique axis and so on. This is a limitation of the way your input, for example using the \fB-y\fR argument of \fBprocess_hkl\fR, is turned into CrystFEL's internal representation of symmetry, and so future versions should very soon be able to handle any setting. + +The options are: + +.IP Triclinic +\fB1\fR, \fB-1\fR. + +.IP Monoclinic +\fB2/m\fR, \fB2\fR, \fBm\fR. + +.IP Orthorhombic +\fBmmm\fR, \fB222\fR, \fBmm2\fR. + +.IP Tetragonal +\fB4/m\fR, \fB4\fR, \fB-4\fR, \fB4/mmm\fR, \fB422\fR, \fB-42m\fR, \fB-4m2\fR, \fB4mm\fR. + +.IP "Trigonal (rhombohedral axes)" +\fB3_R\fR, \fB-3_R\fR, \fB32_R\fR, \fB3m_R\fR, \fB-3m_R\fR. + +.IP "Trigonal (hexagonal axes)" +\fB3_H\fR, \fB-3_H\fR, \fB321_H\fR, \fB312_H\fR, \fB3m1_H\fR, \fB31m_H\fR, \fB-3m1_H\fR, \fB-31m_H\fR. + +.IP Hexagonal +\fB6/m\fR, \fB6\fR, \fB-6\fR, \fB6/mmm\fR, \fB622\fR, \fB-62m\fR, \fB-6m2\fR, \fB6mm\fR. + +.IP Cubic +\fB23\fR, \fBm-3\fR, \fB432\fR, \fB-43m\fR, \fBm-3m\fR. + + .SH PROGRAM NAME There seems to be a tendency to capitalise all the letters in the names of programs in scientific publications. Sometimes the authors do this, other times diff --git a/doc/man/pattern_sim.1 b/doc/man/pattern_sim.1 index b0d2fa06..bd2b35e4 100644 --- a/doc/man/pattern_sim.1 +++ b/doc/man/pattern_sim.1 @@ -30,6 +30,96 @@ The result will be written to an HDF5 file in the current directory with the nam .SH OPTIONS +.PD 0 +.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--gpu\fR +.PD +Use the GPU to speed up the calculation. Requires that OpenCL libraries and drivers are available, and that CrystFEL was compiled with OpenCL enabled. + +.PD 0 +.IP \fB--gpu-dev=\fRIn\fR +.PD +Use GPU device number \fIn\fR. If you omit this option, the list of GPU devices will be shown when you run pattern_sim. + +.PD 0 +.IP "\fB-g\fR \fIfilename\fR" +.IP \fB--geometry=\fR\fIfilename\fR +.PD +Read the detector geometry description from \fIfilename\fR. See \fBman crystfel_geometry\fR for more information. + +.PD 0 +.IP "\fB-b\fR \fIfilename\fR" +.IP \fB--beam=\fR\fIfilename\fR +.PD +Read the beam description from \fIfilename\fR. See \fBman crystfel_geometry\fR for more information. + +.PD 0 +.IP "\fB-n\fR \fn\fR" +.IP \fB--number=\fR\fIn\fR +.PD +Simulate \fIn\fR patterns. Default: \fB-n 1\fR. + +.PD 0 +.IP \fB--no-images\fR +.PD +Do not save any HDF5 files apart from the powder pattern (if requested). + +.PD 0 +.IP "\fB-o\fR \fIfilename\fR" +.IP \fB--output=\fR\fIfilename\fR +.PD +Write the pattern to \fIfilename\fR. The default is \fB--output=sim.5\fR. If more than one pattern is to be simulated (see \fB--number\fR), the filename will be postfixed with a hyphen, the image number and then '.h5'. + +.PD 0 +.IP \fB-r\fR +.IP \fB--random-orientation\fR +.PD +Make up a random orientation for each pattern simulated. + +.PD 0 +.IP \fB--powder=\fR\fIfilename\fR +.PD +Write the sum of all patterns to \fIfilename\fR. + +.PD 0 +.IP "\fB-i\fR \ffilename\fR" +.IP \fB--intensities=\fR\fIfilename\fR +.PD +Get the intensities and phases at the reciprocal lattice points from \fIfilename\fR. + +.PD 0 +.IP "\fB-y\fR \fIpointgroup\fR" +.IP \fB--symmetry=\fR\fIpointgroup\fR +.PD +Use \fIpointgroup\fR as the symmetry of the intensity list (see \fB--intensities\fR). + +.PD 0 +.IP "\fB-t\fR \fImethod\fR" +.IP \fB--gradients=\fR\fImethod\fR +.PD +Use \fImethod\fR as way of calculating the molecular transform between reciprocal lattice points. See the section \fBGRADIENT METHODS\fR below. + +.PD 0 +.IP \fB--really-random\fR +.PD +Seed the random number generator using the kernel random number generator (/dev/urandom). This means that truly random numbers for the orientation and crystal size, instead of the same sequence being used for each new run. + +.PD 0 +.IP \fB--min-size=\fR\fImin\fR +.IP \fB--min-size=\fR\fImax\fR +.PD +Generate random crystal sizes between \fImin\fR and \fImax\fR nanometres. These options must be used together. + +.PD 0 +.IP \fB--no-noise\fR +.PD +Do not calculate Poisson noise. + .SH REFLECTION LISTS @@ -76,6 +166,22 @@ algorithm. When the intensity is sufficiently high that Knuth's algorithm would result in machine precision problems, a normal distribution with standard deviation sqrt(I) is used instead. +.SH GRADIENT METHODS + +The available options for \fB--gradients\fR as as follows: + +.IP \fBmosaic\fR +.PD +Take the intensity of the nearest Bragg position. This is the fastest method and the only one supported on the GPU, but the least accurate. + +.IP \fBinterpolate\fR +.PD +Interpolate trilinearly between six adjacent Bragg intensities. This method has intermediate accuracy. + +.IP \fBphased\fR +.PD +As 'interpolate', but take phase values into account. This is the most accurate method, but the slowest. + .SH AUTHOR This page was written by Thomas White. diff --git a/tests/symmetry_check.c b/tests/symmetry_check.c index 069de582..7c06dfc8 100644 --- a/tests/symmetry_check.c +++ b/tests/symmetry_check.c @@ -322,6 +322,7 @@ int main(int argc, char *argv[]) check_subgroup("432", "23", 1, 1, 2, &fail); check_subgroup("6/m", "-3_H", 1, 1, 2, &fail); check_subgroup("4/m", "-4", 1, 1, 2, &fail); + check_subgroup("622", "321_H", 1, 1, 2, &fail); check_subgroup("4/mmm", "-42m", 1, 1, 2, &fail); check_subgroup("4/mmm", "-4m2", 1, 1, 2, &fail); |