diff options
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/man/indexamajig.1 | 12 | ||||
| -rw-r--r-- | doc/man/process_hkl.1 | 34 |
2 files changed, 35 insertions, 11 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 19a2b942..ba659e7c 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -343,11 +343,13 @@ At the moment, CrystFEL's core symmetry module only knows about one setting for .SH BUGS - Don't run more than one indexamajig jobs simultaneously in the same working directory - they'll overwrite each other's DirAx or MOSFLM files, causing subtle problems which can't easily be detected. - +.PP +The way indexamajig calculates the intensities and errors of peaks sucks, for want of a better word. In particular, I/sigma(I) is not accurately estimated and many of the options don't make sense. Development of improved integration algorithms is in progress, so this issue will be addressed in a future version of CrystFEL. +.PP +ReAx indexing is experimental. It works very nicely for some people, and crashes for others. In a future version, it will be improved and fully supported. .SH AUTHOR This page was written by Thomas White. @@ -368,6 +370,6 @@ You should have received a copy of the GNU General Public License along with Cry .SH SEE ALSO .BR crystfel (7), -.BR check_hkl (1), -.BR compare_hkl (1), -.BR pattern_sim (1) +.BR crystfel_geometry (5), +.BR process_hkl (1), +.BR partialator (1) diff --git a/doc/man/process_hkl.1 b/doc/man/process_hkl.1 index 5e81980d..ea1a77d5 100644 --- a/doc/man/process_hkl.1 +++ b/doc/man/process_hkl.1 @@ -8,20 +8,17 @@ .TH PROCESS\_HKL 1 .SH NAME -process\_hkl \- Monte Carlo merging program +process\_hkl \- Monte Carlo merging of Bragg intensities .SH SYNOPSIS .PP .B process\_hkl -i mypatterns.stream -o mydata.hkl -y mypointgroup [options] .SH DESCRIPTION - -This program takes as input the data stream from "indexamajig". It merges the -many individual intensities together to form a single list of reflection -intensities which are useful for crystallography. +process_hkl takes a data stream from "indexamajig" and merges the many individual intensities together to form a single list of reflection intensities which are useful for crystallography. Typical usage is of the form: - +.PP $ process_hkl -i mypatterns.stream -o mydata.hkl -y mypointgroup .SH CHOICE OF POINT GROUP FOR MERGING @@ -49,3 +46,28 @@ ambiguities to get from the apparent symmetry to the true symmetry (given with The document twin-calculator.pdf contains more detailed information about this issue, as well as tables which contain all the required information. + +.SH AUTHOR +This page was written by Thomas White. + +.SH REPORTING BUGS +Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>. + +.SH COPYRIGHT AND DISCLAIMER +Copyright © 2012 Thomas White <taw@physics.org> +.P +indexamajig is part of CrystFEL. +.P +CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. +.P +CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +.P +You should have received a copy of the GNU General Public License along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. + +.SH SEE ALSO +.BR crystfel (7), +.BR indexamajig (5), +.BR compare_hkl (1), +.BR check_hkl (1), +.BR render_hkl (1), +.BR partialator (1) |