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diff --git a/relnotes-0.6.1 b/relnotes-0.6.1 deleted file mode 100644 index 4c189cd6..00000000 --- a/relnotes-0.6.1 +++ /dev/null @@ -1,165 +0,0 @@ -CrystFEL - Crystallography with a FEL -------------------------------------- - -Release notes for version 0.6.1 - -Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, - a research centre of the Helmholtz Association. - -Authors: - Thomas White <taw@physics.org> - Richard Kirian <rkirian@asu.edu> - Kenneth Beyerlein <kenneth.beyerlein@desy.de> - Andrew Aquila <andrew.aquila@cfel.de> - Andrew Martin <andrew.martin@desy.de> - Lorenzo Galli <lorenzo.galli@desy.de> - Chun Hong Yoon <chun.hong.yoon@desy.de> - Kenneth Beyerlein <kenneth.beyerlein@desy.de> - Karol Nass <karol.nass@desy.de> - Nadia Zatsepin <nadia.zatsepin@asu.edu> - Anton Barty <anton.barty@desy.de> - Cornelius Gati <cornelius.gati@desy.de> - Fedor Chervinskii <fedor.chervinskii@gmail.com> - Alexandra Tolstikova <alexandra.tolstikova@desy.de> - Wolfgang Brehm <wolfgang.brehm@gmail.com> - Valerio Mariani <valerio.mariani@desy.de> - Parker de Waal <Parker.deWaal@vai.org> - Takanori Nakane <nakane.t@gmail.com> - Keitaro Yamashita <k.yamashita@spring8.or.jp> - Oleksandr Yefanov <oleksandr.yefanov@cfel.de> - -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. - -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. - -You should have received a copy of the GNU General Public License along with -CrystFEL. If not, see <http://www.gnu.org/licenses/>. - - -Overview --------- - -The most important new features in this version of CrystFEL are: - -- Introduction of "prediction refinement". - -- Scaling and post-refinement with "partialator". - -- New indexing methods: mosflm-cell and asdf. - -- process_hkl --even-only and --odd-only instead of "alternate-stream". - -These new features have individual sections below. In addition, there are many -other new developments. See the ChangeLog or the changes page on the website -for more details. There were, of course, the usual large number of smaller -refinements and bug fixes. - - -Introduction of "prediction refinement" ---------------------------------------- - -A new refinement step has been introduced between the indexing and prediction/ -integration stages of indexamajig. The refinement aims to maximise the -agreement between the predicted spot positions and the peak positions found by -the peak search step, at the same time as putting the peaks as close to the -Bragg condition as possible. This increases the accuracy of spot prediction, -which has positive effects on the downstream processing stages. - -The prediction refinement stage allows the central beam position to move -relative to the entire detector. The required offset for each crystal is -recorded in the stream and can be visualised using scripts/detector-shift. - -If, somehow, the prediction refinement causes problems for you, you can disable -it using the indexamajig option "--no-refine". - - -Scaling and post-refinement with "partialator" ----------------------------------------------- - -The scaling and post-refinement program partialator is no longer considered -experimental in this version. Many users are already finding significant -improvements in their data simply by applying scaling without partiality: - -$ partialator -i my.stream -o my.hkl -y mypg --model=unity --iterations=3 - -A further improvement is sometimes obtained by applying partialities and doing -full post-refinement: - -$ partialator -i my.stream -o my.hkl -y mypg --model=scsphere --iterations=3 - -Note that partialator applies a per-crystal resolution cutoff to stabilise the -scaling calculation. Therefore, you should experiment with different values -for "--push-res". - -Further improvements to partiality modelling, scaling and merging will be -included in the near future. - - -New indexing methods --------------------- - -This version of CrystFEL can make use of the known unit cell algorithm included -with very recent (7.2.0 or later) versions of mosflm. The known unit cell -algorithm is used by default if you provide lattice parameters to indexamajig. -If this isn't what you want, or if it doesn't work well for you, use -"mosflm-nocell" as your indexing method to restore the old behaviour. - -A new indexing method, asdf, has been added. This algorithm is built into -CrystFEL directly, so no temporary files or external programs are needed. - -The old indexing methods "grainspotter" and "reax" have been removed. - - -process_hkl --even-only and --odd-only --------------------------------------- - -When using process_hkl for merging, you no longer need to use "alternate-stream" -to split the stream into two parts in order to calculate figures of merit such -as Rsplit. Instead, simply use the "--even-only" and "--odd-only" options to -merge only even-numbered and odd-numbered crystals from the stream: - -$ process_hkl -i my.stream -o my.hkl1 -y mypg --even-only -$ process_hkl -i my.stream -o my.hkl2 -y mypg --odd-only -$ compare_hkl my.hkl1 my.hkl2 -y mypg --fom=rsplit [..etc..] - -Note that the numbering of crystals for this purpose is simply according to the -order they appear in the stream. For most purposes, this is effectively random. - -Note further that partialator writes the ".hkl1" and ".hkl2" split-merged -datasets for you automatically. - - -API changes ------------ - -The following changes have been made to the libcrystfel API: - -New functions: - - asdf_prepare(), run_asdf(), asdf_cleanup() - - cell_get_volume() - - crystal_{get,set}_Bfac() - - crystal_{get,set,add}_notes() - - detector_has_clen_references() - - {x,y,r}_gradient() - - refine_prediction() - - refine_radius() - - {get,set}_panel() - - {get,set}_flag() - - solve_svd() - -Removed functions: - - select_intersections() - - update_partialities_2() - - get_excitation_error() - - extract_f_from_stuff() - - grainspotter_{prepare,index,cleanup}() - - reax_{prepare,index,cleanup}() - -Changed function prototypes: - - integrate_all_4() - - set_detector_pos() |