From 5d2470908016d64b449eda5f010d8e24db62fc73 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Wed, 17 Apr 2024 15:17:02 +0200 Subject: Update crystfel(7) --- doc/man/crystfel.7 | 50 +++++++++++++++++++++++++++----------------------- 1 file changed, 27 insertions(+), 23 deletions(-) diff --git a/doc/man/crystfel.7 b/doc/man/crystfel.7 index 3ff25c16..a03ea0bc 100644 --- a/doc/man/crystfel.7 +++ b/doc/man/crystfel.7 @@ -1,7 +1,7 @@ .\" .\" CrystFEL main man page .\" -.\" Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY, +.\" Copyright © 2012-2024 Deutsches Elektronen-Synchrotron DESY, .\" a research centre of the Helmholtz Association. .\" .\" Part of CrystFEL - crystallography with a FEL @@ -9,23 +9,14 @@ .TH CRYSTFEL 7 .SH NAME -CrystFEL \- data processing for FEL crystallography +CrystFEL \- data processing for serial crystallography .SH DESCRIPTION -CrystFEL is a suite of programs for processing Bragg diffraction data acquired with a free electron laser in a "serial" manner. Some of the particular characteristics of such data which call for a specialised software suite are: +CrystFEL is a suite of programs for processing data from serial crystallography +experiments, performed at synchrotron and X-ray free-electron laser facilities, +as well as in your home lab using an electron microscope. -.RS -Each crystal is used for only one exposure, and there is no oscillation, rotation nor a large bandwidth or divergence. Therefore, many or all reflections are partially integrated. -.PP -The crystals might be very small and the illumination highly coherent, leading to significant Fourier truncation effects on the detector. -.PP -Many patterns, numbering tens of thousands or more, are required, so high throughput automated processing is important. -.PP -The crystal orientations in each pattern are random and uncorrelated, which leads to special considerations during scaling and merging. -.RE - -CrystFEL includes programs processing patterns subject to the above -characteristics. The programs are: +The programs in the suite are: .IP \fBindexamajig\fR Batch indexing, integration and data reduction program, which produces a "stream" containing the indexing and integration results for each diffraction pattern. @@ -54,7 +45,7 @@ Tools for calculating figures of merit, such as completeness and R-factors. .IP \fBrender_hkl\fR A tool for rendering slices of reciprocal space in two dimensions. -.IP \fBgeoptimiser\fR +.IP \fBalign_detector\fR A program to refine and optimize detector geometry. .IP \fBlist_events\fR @@ -64,7 +55,10 @@ A tool for creating lists of events from multi-event data files. A tool for locating runs of crystals with similar orientations, e.g. from 'mini rotation series' arising from the use of a slow extrusion sample injector. .IP \fBmake_pixelmap\fR -A tool for for creating pixel maps for Cheetah, OnDA etc. +A tool for creating pixel maps for Cheetah, OnDA etc. + +.IP \fBadjust_detector\fR +A tool to alter detector geometry. .PP There is also a folder full of scripts for achieving many related tasks. @@ -123,13 +117,24 @@ to this list if you experience difficulty with "-y" at any time. \fB23\fR, \fBm-3\fR, \fB432\fR, \fB-43m\fR, \fBm-3m\fR. .SH FUNDING ACKNOWLEDGEMENTS -Development of CrystFEL is primarily funded by the Helmholtz Association via programme-oriented funds. +Development of CrystFEL is primarily funded by the Helmholtz Association via DESY. + +Partial funding for CrystFEL has been provided by: + +* The consortium DAPHNE4NFDI in the context of the work of the NFDI e.V. The + consortium is funded by the Deutsche Forschungsgemeinschaft (DFG, German + Research Foundation) - project number 460248799 (2022-). + +* European Union’s Horizon 2020 research and innovation programme under grant + agreement No 857641 (ExPaNDS) (2019-2023). -Additional funding for CrystFEL is provided by "X-Probe", a project of the European Union's 2020 Research and Innovation Program Under the Marie Skłodowska-Curie grant agreement 637295 (2015-2018). +* X-Probe, a project of the European Union's 2020 Research and Innovation + Program Under the Marie Skłodowska-Curie grant agreement 637295 (2015-2018). -Additional funding for CrystFEL is provided by the BMBF German-Russian Cooperation "SyncFELMed", grant 05K14CHA (2014-2017). +* The BMBF German-Russian Cooperation SyncFELMed, grant 05K14CHA (2014-2017). -Past funding for CrystFEL has been received from BioStruct-X, a project funded by the Seventh Framework Programme (FP7) of the European Commission. +* BioStruct-X, a project funded by the Seventh Framework Programme (FP7) of the + European Commission (2011-2016). .SH AUTHOR This page was written by Thomas White and Valerio Mariani. @@ -139,7 +144,7 @@ Report bugs to , or visit .SH COPYRIGHT AND DISCLAIMER .PD 0 -Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. +Copyright © 2012-2024 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. .PD .PP Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and contributors. @@ -159,7 +164,6 @@ You should have received a copy of the GNU General Public License along with Cry .BR render_hkl (1), .BR get_hkl (1), .BR cell_tool (1), -.BR geoptimiser (1), .BR whirligig (1), .BR list_events (1), .BR make_pixelmap (1), -- cgit v1.2.3