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diff --git a/doc/man/partialator.1 b/doc/man/partialator.1 index decaa07c..aa25d2a7 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, overriding the values from the stream. 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. +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. -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. - - -.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 @@ -174,15 +190,15 @@ partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=uni .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 +partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=xsphere --iterations=0\fR .IP "Merging with partialities, with scaling but without post-refinement:" .PD -partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=1 --no-pr\fR +partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=xsphere --iterations=1 --no-pr\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 +partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=xsphere --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) @@ -190,11 +206,9 @@ partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scs .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 +partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=xsphere --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 CUSTOM DATASET SPLITTING When performing a time-resolved experiment (for example), it is preferable to ensure that the data for all time points has been processed identically. Rather than processing each time point independently with separate runs of partialator, it is better to process them all together and do the splitting into time points just before the final output. Consider, for example, the case of simple scaling (without a B factor): when merging independently, the resulting datasets would probably end up with different overall scaling factors. When comparing the results, you would need to take this difference into account. In practice, most programs can do that job easily, but what about if a B factor is included? And what if partialities are included - how unique is the solution? @@ -216,7 +230,7 @@ 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 |