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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
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