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diff --git a/relnotes-0.6.2 b/relnotes-0.6.2 new file mode 100644 index 00000000..daf48f3f --- /dev/null +++ b/relnotes-0.6.2 @@ -0,0 +1,154 @@ +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. |