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diff --git a/relnotes-0.7.0 b/relnotes-0.7.0 deleted file mode 100644 index 186694a0..00000000 --- a/relnotes-0.7.0 +++ /dev/null @@ -1,176 +0,0 @@ -CrystFEL - Data processing for serial crystallography ------------------------------------------------------ - -Release notes for version 0.7.0 - -Copyright © 2012-2018 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> - 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> - Steve Aplin <steve.aplin@desy.de> - Helen Ginn <helen@strubi.ox.ac.uk> - Thomas Grant <tgrant@hwi.buffalo.edu> - Mamoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp> - -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: - -- New options system for indexamajig, removing most of the profusion of indexing - method flags "comb", "bad", "retry" and so on. Indexamajig can also now - automatically determine which indexing methods can be used if you don't tell - it which ones to use. In addition, the options for the Felix indexing method - have now been greatly simplified. - -- The spectrum-based partiality model and numerical post-refinement algorithm - from Ginn et al [Acta D71 2015 p1400] was incorporated. - -- The symmetry of the merged reflection list is now tracked through automatically, - so you no longer need to give the "-y" option to compare_hkl and check_hkl. - -These changes have sections below. In addition, there were many bug fixes and -other improvements. See the "ChangeLog" or the changes page on the CrystFEL -website for details. - - -New indexamajig options system ------------------------------- - -The new version of indexamajig will automatically determine which indexing -methods to use based on the prior information (e.g. if a target unit cell was -provided) and which indexing programs are available on the computer. To enable -the automatic determination, simply omit any "--indexing=" option to indexamajig. -Of course, you can override the automatic choice by specifying --indexing, just -as it worked before. - -To options for finer control of the indexing process, which in previous versions -were enabled or disabled by adding flags to the indexing methods -(e.g. "mosflm-noretry"), now apply to all indexing methods at once and are -selected using new options, listed below. - -The indexing method should contain only the method itself and prior information -modifiers ('cell' or 'latt'). This simplifies things greatly by removing the -very long indexing method descriptions ("mosflm-raw-latt-noretry-refine-nomulti" -and so on). - -- To disable prediction refinement ('norefine'), use --no-refine. -- To check cell axes only ('axes'), use --no-cell-combinations. -- To disable all unit cell checks ('raw'), use --no-check-cell. -- To disable peak alignment check ('bad'), use --no-check-peaks. -- To disable indexing retry ('noretry'), use --no-retry. -- To enable multi-lattice indexing by 'delete and retry', use --multi. - - -Spectrum-based partiality model and post-refinement ---------------------------------------------------- - -This version includes an implementation of the spectrum-based partiality model -described by Ginn et al., Acta D71 2015 p1400 and associated numerical post- -refinement algorithm. To use it, use "partialator --model=xsphere". The old -models (scsphere and scgaussian) have been removed. You will probably need to -experiment with changing the bandwidth and reflection radius, using ---force-bandwidth and --force-radius. Add --no-pr to disable post-refinement, -while still using the partiality estimates. To use post-refinement, omit --no-pr, -but you should also run indexamajig with "--overpredict". You may also need to -disable B factor scaling in partialator with "--no-Bscale". - -If you use post-refinement, the new scripts "plot-pr" and "plot-contourmap" can -be used to visualise the distributions of partialities and the contour maps of -residual against parameters such as crystal rotation angle. The data for these -graphs is in the "pr-logs" folder which will be created by partialator. - -Partiality modelling and post-refinement should still be considered experimental -when applied to real data. The success of post-refinement depends on many -factors, and only has a chance of working if there are no other problems with -the dataset (e.g. inaccurate detector geometry). Further improvements should -appear in future versions. - - -Automatic tracking of reflection list symmetry ----------------------------------------------- - -The point group symmetry used for merging a reflection list has been stored in -the reflection file (.hkl) for a long time. However, version 0.7.0 of CrystFEL -uses the stored symmetry when performing tasks such as calculating figures of -merit using check_hkl. You can simply omit the "-y" options which were needed -previously. Of course, you can override the symmetry by specifying -y as before. - - -API changes ------------ - -The following changes have been made to the libcrystfel API. - -New functions: - - asdf_probe() and _probe for all other indexing methods. - - compare_cells() - - crystal_get_cell_const() - - crystal_get_profile_radius() - - predict_to_res() - - calculate_partialities() - - update_predictions() - - is_cbf_file() - - get_indm_from_string_2() - - detect_indexing_methods() - - integrate_all_5() - - read_reflections_2() - - {get,set}_{khalf,kpred,exerr}() - - first_refl_const(), next_refl_const() - - open_stream_for_write_4() - - stream_has_old_indexers() - - stream_audit_info() - -Removed functions: - - find_intersections() - - find_intersections_to_res() - - update_partilities() - - write_reflections_to_file() - - read_reflections_from_file() - - {get,sh}_partial() - -Changed function prototypes: - - asdf_prepare() and _prepare for all other indexing methods. - - cell_new_from_cell() (input UnitCell is now const) - - crystal_copy() (input Crystal is now const) - - x_gradient(), y_gradient() - - remove_flagged_crystals() (now returns number of crystals removed) - - setup_indexing() - -Changed structure/enum definitions: - - PartialityModel: removed PMODEL_SCSPHERE and PMODEL_SCGAUSSIAN, - added PMODEL_XSPHERE - - gparam: added GPARAM_ANG1, GPARAM_ANG2, GPARAM_WAVELENGTH, GPARAM_EOL - - Added IndexingFlags |