diff options
| author | Thomas White <taw@physics.org> | 2013-05-02 16:43:22 +0200 |
|---|---|---|
| committer | Thomas White <taw@physics.org> | 2013-05-02 16:43:22 +0200 |
| commit | a4bdd1335ffc98e885126af5468b0696396479cf (patch) | |
| tree | 43fe08d1ccb8f22acfd962f6302713e9ff2ddf6f /doc | |
| parent | c5bcfa0ae036145f23c344796f8b4efcee69429a (diff) | |
| parent | 6b18fa18fbdc1f272e65f81d04b22d973acafa1e (diff) | |
Merge branch 'tom/partials'
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/man/partial_sim.1 | 22 | ||||
| -rw-r--r-- | doc/reference/libcrystfel/CrystFEL-sections.txt | 6 |
2 files changed, 25 insertions, 3 deletions
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1 index 5b417978..7321b9ff 100644 --- a/doc/man/partial_sim.1 +++ b/doc/man/partial_sim.1 @@ -1,7 +1,7 @@ .\" .\" partial_sim man page .\" -.\" Copyright © 2012 Thomas White <taw@physics.org> +.\" Copyright © 2012-2013 Thomas White <taw@physics.org> .\" .\" Part of CrystFEL - crystallography with a FEL .\" @@ -77,6 +77,24 @@ Add random values with a flat distribution to the components of the reciprocal l .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 +.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 +.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 \fR--input\fB. + +.PD 0 +.B +.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. + .SH AUTHOR This page was written by Thomas White. @@ -84,7 +102,7 @@ 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 © 2012-2013 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. .P partial_sim, and this manaul, are part of CrystFEL. .P diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index 720cabff..09267538 100644 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -21,10 +21,11 @@ next_found_refl get_excitation_error get_detector_pos get_partiality +get_lorentz +get_partial get_indices get_symmetric_indices get_intensity -get_partial get_scalable get_refinable get_redundancy @@ -34,6 +35,8 @@ get_temp1 get_temp2 <SUBSECTION> set_detector_pos +set_partiality +set_lorentz set_partial set_intensity set_scalable @@ -380,6 +383,7 @@ crystal_set_user_flag <SECTION> <FILE>geometry</FILE> +PartialityModel find_intersections select_intersections update_partialities |