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diff --git a/relnotes-0.6.1 b/relnotes-0.6.1 new file mode 100644 index 00000000..4c189cd6 --- /dev/null +++ b/relnotes-0.6.1 @@ -0,0 +1,165 @@ +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() |