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diff --git a/doc/man/partialator.1 b/doc/man/partialator.1 index decaa07c..0a5b78ba 100644 --- a/doc/man/partialator.1 +++ b/doc/man/partialator.1 @@ -1,7 +1,7 @@ .\" .\" partialator man page .\" -.\" Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, +.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, .\" a research centre of the Helmholtz Association. .\" .\" Part of CrystFEL - crystallography with a FEL @@ -132,29 +132,45 @@ Reject crystals if the absolute values of their relative Debye-Waller ("B") fact .PD Write out the per-crystal parameters and reflection lists after every cycle of refinement, instead of only at the end. The intermediate reflection lists and parameter filenames will be prefixed with \fBiter\fIN\fB_\fR (note the trailing underscore), where \fIN\fR is the iteration number. If you use \fB--custom-split\fR, intermediate results will also be output for each custom dataset. +.PD 0 +.IP \fB--no-logs\fR +.PD +Do not write the extensive log files needed for plotting contour maps and spectrum graphs. This makes the process a lot faster, but you probably do want these logs to check that post-refinement is working reasonably. + +.PD 0 +.IP "\fB-w\fR \fIpg\fR" +.PD +Set the apparent symmetry of the crystals. The ambiguity operator will be determined by comparing this to the actual symmetry. +.IP +If you prefer (or the scenario demands it), you can specify the ambiguity operator directly using \fB--operator\fR. + +.PD 0 +.IP \fB--operator=\fR\fIop\fR +.PD +Specify the indexing ambiguity operator. Example: \fB--operator=k,h,-l\fR. +.IP +If you prefer, you can specify the ambiguity operator by specifying the apparent symmetry using \fB-w\fR. + +.PD 0 +.IP \fB--force-bandwidth=\fIbw\fR +.IP \fB--force-radius=\fIR\fR +.PD +Set the X-ray bandwidth or initial profile radius for all crystals before proceeding. 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. + .SH PARTIALITY MODELS The available partiality models are: -.IP \fBscsphere\fR +.IP \fBxsphere\fR .PD 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" 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, -and in Phil. Trans. Roy. Soc. B 369 (2014) 20130330, except that the "Lorentz -factor" described there is no longer treated as a separate factor. +source for the reflection. The X-ray spectrum is modelled as a super-Gaussian +with exponent 1.5, and the overlap integral is evaluated numerically. - -.IP \fBscgaussian\fR -.PD -As \fBscsphere\fR, except that the shape of the scattering density centered on -each reciprocal lattice point is taken to be a 3D Gaussian distribution instead -of a sphere. The standard deviation of the distribution will be the profile -radius (determined by indexamajig) divided by 2.6. +This model is the same as that described in Acta Cryst. D71 (2015) p1400. .IP \fBunity\fR .PD @@ -216,7 +232,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. +Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. .P partialator, and this manual, are part of CrystFEL. .P |