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diff --git a/relnotes-0.6.2 b/relnotes-0.6.2 deleted file mode 100644 index daf48f3f..00000000 --- a/relnotes-0.6.2 +++ /dev/null @@ -1,154 +0,0 @@ -CrystFEL - Crystallography with a FEL -------------------------------------- - -Release notes for version 0.6.2 - -Copyright © 2012-2016 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: - -- Stability improvements to the scaling algorithm in partialator. - -- Addition of "custom dataset splitting" in partialator. - -- "retry" indexing. - -- Per-pixel saturation values - -These changes have sections below. In addition, there were many bug fixes and -smaller improvements. - - -Stability improvements in partialator -------------------------------------- - -The scaling algorithm in partialator has been altered such that only the strong -reflections contribute to the scaling factors at all. This reduces the -"drifting" of scale factors which happened before, and helps avoid the situation -where a very large number of crystals get rejected with large B factors. -Of course, all reflections contribute to the final merged data set as before. - -In CrystFEL 0.6.1, we needed to reduce the amount of noise going into the -scaling algorithm to make it work. This was done by including reflections only -up to the apparent (conservative) resolution limit of each crystal made by -indexamajig, and could be overridden by using the "--push-res" option of -partialator. The default --push-res value was zero, which meant to ignore any -reflections higher than the limit. With the stabilised algorithm, this is no -longer necessary, and hence the default --push-res value has been changed to -infinity, i.e. no cutoff at all. You can restore the old behaviour with ---push-res=0. - - -Custom dataset splitting in partialator ---------------------------------------- - -When performing a time-resolved or isomorphous replacement experiment (plus some -other types of experiment), it is preferable to ensure that the data for all -time points has been processed identically. Rather than processing each time -point independently with separate runs of partialator, it is better to process -them all together and do the splitting into time points just before the final -output. Consider, for example, the case of simple scaling (without a B -factor): when merging independently, the resulting datasets would probably end -up with different overall scaling factors. When comparing the results, you -would need to take this difference into account. In practice, most programs -can do that job easily, but what about if a B factor is included? And what if -partialities are included - how unique is the solution? - -Partialator's new "custom dataset splitting" option allows you to provide a -text file containing a list of filenames, event numbers and dataset -names, one event (detector frame) per line. All crystals will be refined -together, but they will be merged according to the dataset names you give. The -parameters (scaling factors, partialities etc) determined during the joint -refinement will be applied. For each dataset, a separate pair of split -half-datasets will also be written, allowing you to calculate figures of merit -such as Rsplit and CC1/2 for each one. - - -"retry" indexing ----------------- - -If an indexing method fails to index a pattern (or if the solution doesn't get -through the prediction refinement stage), this version of CrystFEL will delete -the weakest few peaks and try again. This can increase the indexing yield a lot -(sometimes a factor of two!), but decreases the speed. If you'd rather keep -things fast, add "-noretry" to each of your indexing methods. - - -Per-pixel saturation values ---------------------------- - -When using dual-gain mode on the CSPAD (or any other detector which offers a -similar feature), our current advice is to correct the pixel values in one of -the regions by multiplying them by the relative gain factor. This will give -image data which looks good, but the saturation values will be different in the -two regions. To handle this, CrystFEL 0.6.2 allows you to prepare a map, in -HDF5 format, giving the saturation value for each pixel individually. The -script "gaincal-to-saturation-map" can be used to create a suitable file from -the gain map (e.g. as generated and used by Cheetah). Specify the filename and -HDF5 path of the saturation map using saturation_map and saturation_map_file -in the geometry file - these work exactly like the bad pixel map. Reflections -containing any pixel above this value will be rejected, in addition to any -reflections which get rejected by the usual saturation criteria (so remove any -max_adu directives if you want the saturation map to be the only decider!). - - -API changes ------------ - -The following changes have been made to the libcrystfel API: - -New functions: - - write_cell() - - find_orig_panel_number() - - felix_{prepare,index,cleanup}() - - sort_peaks() - - remove_flagged_crystals() - - open_stream_for_write_3() - -Removed functions: - (none) - -Changed function prototypes: - - prepare_indexing() - -"data", "flags" and "twotheta" were removed from "struct image", and "sat" was -added. |