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February 2022

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Subject	From	Date	Size
[git/cctbx_project] master: Added the Planck constant and neutron mass to scitbx/constants.h (21013935b3)	CCTBX commit	Mon, 28 Feb 2022 09:27:54 -0800	100 lines
[git/cctbx_project] master: Change order of vectors on the vectors tab putting rotation vectors at the end. When zooming in clip plane mode mouse movement should be the same as when using trackballcontrol. (62c2c1d259)	CCTBX commit	Sun, 27 Feb 2022 20:42:52 +0000	176 lines
[git/dxtbx] main: Clean Clutter (047411c2)	DXTBX commit	Sun, 27 Feb 2022 19:35:44 +0000	89 lines
[git/cctbx_project] master: Don't autozoom when clicking to show mates of a reflection with respect to a rotation operator (84c14a4dec)	CCTBX commit	Sat, 26 Feb 2022 00:51:49 +0000	746 lines
[git/cctbx_project] master: bootstrap: add Colabs to PhenixBuilder (f36b6de540)	CCTBX commit	Thu, 24 Feb 2022 14:12:37 -0800	115 lines
[git/dxtbx] main: Add filtering by event code to FormatXTC (#489) (924160b5)	DXTBX commit	Thu, 24 Feb 2022 13:57:26 -0800	433 lines
[git/dxtbx] main: Proper default for FormatXTC's delta_k (#490) (a6a15f38)	DXTBX commit	Thu, 24 Feb 2022 13:05:16 -0800	107 lines
[git/cctbx_project] master: Avoid assigning camera.zoom to NaN. Avoid MS font by manual editing output from Qtdesigner (15bef16dbc)	CCTBX commit	Thu, 24 Feb 2022 17:38:54 +0000	625 lines
[git/cctbx_project] master: Reduce2 info rebase (#735) (045ab24f10)	CCTBX commit	Thu, 24 Feb 2022 08:31:23 -0500	344 lines
[git/cctbx_project] master: minor PRIME fix (import) (c8bbf29420)	CCTBX commit	Wed, 23 Feb 2022 17:05:58 -0800	88 lines
[git/cctbx_project] master: fixed imports to match new IOTA tree (ad23ecb690)	CCTBX commit	Wed, 23 Feb 2022 15:51:34 -0800	311 lines
[git/dxtbx] main: Add get_spectrum to FormatXTC (#484) (8d9a4623)	DXTBX commit	Wed, 23 Feb 2022 11:53:55 -0800	327 lines
[git/cctbx_project] master: XFEL GUI: fix rare use case for job submit (a00af8a6eb)	CCTBX commit	Wed, 23 Feb 2022 11:47:57 -0800	98 lines
[git/cctbx_project] master: CCTBXParser: unused_phil_raises_sorry also hides unrecognized parameters (014edc3655)	CCTBX commit	Tue, 22 Feb 2022 23:34:00 -0800	97 lines
[git/cctbx_project] master: fix for 6eym and alike (007a755a05)	CCTBX commit	Tue, 22 Feb 2022 16:59:06 -0800	89 lines
[git/cctbx_project] master: Using camera.zoom instead of NGL.trackballzoom to avoid unexpected display of reflections that should be outside the frustum when using clip planes (d1d5da4146)	CCTBX commit	Wed, 23 Feb 2022 00:47:01 +0000	801 lines
[git/cctbx_project] master: Skip test if required folder is missing (948ce1b338)	CCTBX commit	Tue, 22 Feb 2022 16:41:21 -0800	95 lines
[git/cctbx_project] master: interactive peak picking in powder_from_spots (#730) (3379ff0acb)	CCTBX commit	Tue, 22 Feb 2022 12:14:01 -0500	341 lines
[git/dxtbx] main: Update pre-commits - Take 2 (#468) (a7e24045)	DXTBX commit	Tue, 22 Feb 2022 15:40:47 +0000	2902 lines
[git/dxtbx] main: DIALS 3.8.3 Changelog (c07d8d30)	DXTBX commit	Tue, 22 Feb 2022 15:19:16 +0000	110 lines
[git/cctbx_project] master: Fix bugs in handling of argparse output. (7c284f7395)	CCTBX commit	Tue, 22 Feb 2022 10:06:09 +0000	148 lines
[git/cctbx_project] master: Substituting datatypes with column names whenever data column type is a generic data type such as floating point or int. Button for deleting user settings and using factory defaults. Function for making new factory default settings. (63a4716822)	CCTBX commit	Mon, 21 Feb 2022 23:37:12 +0000	1001 lines
[git/cctbx_project] master: Add options to define the sphere enclosing a model and to flatten the density under a model. (51383fa2e6)	CCTBX commit	Mon, 21 Feb 2022 19:33:33 +0000	519 lines
[git/dxtbx] main: Allow non-dark corrected cspad data in FormatXTCCspad (#479) (974f9651)	DXTBX commit	Mon, 21 Feb 2022 10:19:52 +0000	116 lines
[git/cctbx_project] master: Factory defaults for QT GUI, colour and radii settings. Include computed length of vectors to be displayed in the list of tuples representing vectors that can be used for aligning clip planes (for the sake of tNCS vector where length should be the inverse of the reciprocal space vector length). (a94df6d4a4)	CCTBX commit	Mon, 21 Feb 2022 01:27:51 +0000	97 lines
[git/cctbx_project] master: Catch missing symmetry (2a3a3deb18)	CCTBX commit	Sat, 19 Feb 2022 16:35:16 -0800	105 lines
[git/cctbx_project] master: correct path (922f159cfe)	CCTBX commit	Fri, 18 Feb 2022 18:22:10 -0800	88 lines
[git/cctbx_project] master: merge per model (9f619b7d1f)	CCTBX commit	Fri, 18 Feb 2022 18:21:31 -0800	162 lines
[git/cctbx_project] master: test for D terminii (eab1d8fcbf)	CCTBX commit	Fri, 18 Feb 2022 15:06:40 -0800	623 lines
[git/cctbx_project] master: fixes for D atom terminii with test (dbd3bea6ac)	CCTBX commit	Fri, 18 Feb 2022 15:06:06 -0800	238 lines
[git/cctbx_project] master: Move print to inside verbose only (0f06acfa63)	CCTBX commit	Fri, 18 Feb 2022 13:08:23 -0800	104 lines
[git/dxtbx] main: Float beam centre (#487) (aecc59cc)	DXTBX commit	Fri, 18 Feb 2022 15:55:14 +0000	156 lines
[git/cctbx_project] master: CCTBXParser: avoid replacing variable name (96b65655b1)	CCTBX commit	Thu, 17 Feb 2022 12:21:51 -0800	148 lines
[git/cctbx_project] master: CCTBXParser: allow subclass in run_program (2f2f5533ab)	CCTBX commit	Thu, 17 Feb 2022 11:48:51 -0800	577 lines
[git/dxtbx] main: Drop datablocks from radial average (#480) (1031bc64)	DXTBX commit	Thu, 17 Feb 2022 08:05:18 -0800	168 lines
[git/cctbx_project] master: CCTBXParser: add parameter to continue when unused PHIL are found (5ca5c8928c)	CCTBX commit	Wed, 16 Feb 2022 14:53:59 -0800	451 lines
[git/dxtbx] main: ImageSequence slicing: handle negative offset (#485) (67aab217)	DXTBX commit	Wed, 16 Feb 2022 16:14:19 -0500	250 lines
[git/cctbx_project] master: XFEL GUI: add detz_offset for Jungfrau4M at LCLS (a1688b88ba)	CCTBX commit	Wed, 16 Feb 2022 12:43:22 -0800	97 lines
[git/cctbx_project] master: Allow flexibility when extracting flags (2d21e46564)	CCTBX commit	Wed, 16 Feb 2022 11:58:18 -0800	167 lines
[git/cctbx_project] master: Fix bug in code to create mask for ordered density. (b4aedc6194)	CCTBX commit	Wed, 16 Feb 2022 19:30:59 +0000	131 lines
[git/cctbx_project] master: Add filtering to mosaic, and a bug fix (36bdc226ec)	CCTBX commit	Wed, 16 Feb 2022 10:57:50 -0800	317 lines
[git/cctbx_project] master: skip if skip (72d786001c)	CCTBX commit	Wed, 16 Feb 2022 09:44:40 -0800	89 lines
[git/cctbx_project] master: show_all_vectors() for quickly displaying or removing all rotation operators. (f61c3a59ca)	CCTBX commit	Tue, 15 Feb 2022 21:51:01 +0000	602 lines
[git/cctbx_project] master: clean clutter (e44d933411)	CCTBX commit	Tue, 15 Feb 2022 10:33:52 -0800	84 lines
[git/cctbx_project] master: missed some phil details (46fc5028e8)	CCTBX commit	Tue, 15 Feb 2022 09:38:21 -0800	93 lines
[git/cctbx_project] master: better class org. (be1372037a)	CCTBX commit	Mon, 14 Feb 2022 16:46:08 -0800	1072 lines
[git/cctbx_project] master: big changes to QI including strain energies (179e717357)	CCTBX commit	Mon, 14 Feb 2022 16:45:26 -0800	2780 lines
[git/cctbx_project] master: Remove unused import (43ed2f08c4)	CCTBX commit	Mon, 14 Feb 2022 16:35:36 -0800	85 lines
[git/cctbx_project] master: Fix functionality to add *_wfc_obj.pkl files and add a test (19d825cba9)	CCTBX commit	Mon, 14 Feb 2022 16:03:41 -0800	190 lines
[git/cctbx_project] master: Fixed incorrect string of the equation of plane of visible reflections when applying clip planes (db685f4400)	CCTBX commit	Mon, 14 Feb 2022 20:02:20 +0000	1567 lines
[git/cctbx_project] master: Improve calculation of over_sampling_factor: more in line with crystallographic likelihoods where about half of volume is typically ordered structure. (f0aedab32c)	CCTBX commit	Mon, 14 Feb 2022 14:21:24 +0000	191 lines
[git/cctbx_project] master: CI: add SKIP_CACHED_BUILD to XFEL CI (3fa571098a)	CCTBX commit	Sun, 13 Feb 2022 23:23:56 -0800	309 lines
[git/cctbx_project] master: CI: update mirror (f05c69a188)	CCTBX commit	Sun, 13 Feb 2022 19:26:52 -0800	103 lines
[git/cctbx_project] master: I naively assume that D is the same as H in this context. (4b30c88f78)	CCTBX commit	Sat, 12 Feb 2022 12:30:04 -0800	74 lines
[git/cctbx_project] master: Catch c++ error that can happen on colabs: Another associated atom_tmp_sentinel instance still exists (ca76da989b)	CCTBX commit	Sat, 12 Feb 2022 07:33:16 -0700	125 lines
[git/cctbx_project] master: Bug fix for speed issue: Avoid deep copying arrays when expanding reflections in browser. (433fbd35cf)	CCTBX commit	Sat, 12 Feb 2022 00:23:47 +0100	301 lines
[git/dxtbx] main: Revert "Never install dxtbx into conda_base/ when running under libtbx (#474)" (#483) (20100530)	DXTBX commit	Fri, 11 Feb 2022 09:54:08 +0000	426 lines
[git/cctbx_project] master: helper function (full D or not) and allow D in rotamer fitting (e785246fb4)	CCTBX commit	Thu, 10 Feb 2022 17:52:12 -0800	130 lines
[git/cctbx_project] master: adds option to mask pixels outside trusted range (bd852daf3e)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	247 lines
[git/cctbx_project] master: fixes test (3d5399cec0)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	248 lines
[git/cctbx_project] master: updates to ensemble data loader (3c1d228ac0)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	244 lines
[git/cctbx_project] master: fixes restraints bug in stage_two_utils (871496f00e)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	103 lines
[git/cctbx_project] master: gives parameters a new attribute is_global (26e4db9699)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	152 lines
[git/cctbx_project] master: updates to hopper utils (e13adb2fcd)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	728 lines
[git/cctbx_project] master: updates to diffBragg forward model func (42a0b897b2)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	227 lines
[git/cctbx_project] master: GPU wavelength image (bca9cc4ce0)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	388 lines
[git/cctbx_project] master: allows switching conventions when writing CBF (92541aa87c)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	198 lines
[git/cctbx_project] master: Updates to simtbx.diffBragg.hopper (abc5b82030)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	284 lines
[git/cctbx_project] master: adds more control for modeling detector thickness (06e9115742)	CCTBX commit	Thu, 10 Feb 2022 15:23:11 -0600	356 lines
[git/cctbx_project] master: clean other clutter (a3ae893f3c)	CCTBX commit	Thu, 10 Feb 2022 10:31:26 -0800	82 lines
[git/cctbx_project] master: clean clutter (409ed01440)	CCTBX commit	Thu, 10 Feb 2022 10:30:05 -0800	86 lines
[git/dxtbx] main: Never install dxtbx into conda_base/ when running under libtbx (#474) (cbe9fa9e)	DXTBX commit	Thu, 10 Feb 2022 17:20:14 +0000	428 lines
[git/cctbx_project] master: Remove unused line (764067520b)	CCTBX commit	Thu, 10 Feb 2022 16:40:28 +0000	87 lines
[git/cctbx_project] master: Change masking of ordered density so that it uses a Z-score (ratio of local mean density squared to local mean noise squared), where the noise is estimated from the difference between half maps. This compensates for the frequent occurrence of maps that are masked to fall off towards the edges and corners. (c68a3a3b48)	CCTBX commit	Thu, 10 Feb 2022 16:40:28 +0000	663 lines
[git/dxtbx] main: Move Azure Pipelines CI to use the CMake build (#482) (f295e390)	DXTBX commit	Thu, 10 Feb 2022 15:59:22 +0000	222 lines
[git/dxtbx] main: Add format class for I19-2 Eiger with DAC shadow (#481) (5cf1b921)	DXTBX commit	Thu, 10 Feb 2022 13:35:16 +0000	312 lines
[git/cctbx_project] master: Bug fix for sliding clip planes along incorrect axis, Persisting wrap mode of textinfo. (95709a73aa)	CCTBX commit	Thu, 10 Feb 2022 00:28:57 +0000	572 lines
[git/cctbx_project] master: Bugfix (d7f183e08e)	CCTBX commit	Wed, 9 Feb 2022 13:26:41 -0800	93 lines
[git/cctbx_project] master: Add try/except to cctbx.xfel.mpi_integrate (31386f7fad)	CCTBX commit	Wed, 9 Feb 2022 09:43:06 -0800	179 lines
[git/cctbx_project] master: rough draft of new merging worker modify_reindex_to_abc (d5e8d2dbcf)	CCTBX commit	Wed, 9 Feb 2022 09:41:59 -0800	263 lines
[git/cctbx_project] master: tmp disable untill I know what the test wants (7f4ab6df92)	CCTBX commit	Tue, 8 Feb 2022 18:29:45 -0800	149 lines
[git/cctbx_project] master: Making it more flexible (282793d68d)	CCTBX commit	Tue, 8 Feb 2022 18:02:32 -0800	172 lines
[git/cctbx_project] master: Simple frustum culling calculation for listing visible hkls within clipNear and clipFar. Hiding slice mode which is now superseeded by positioning clip planes exactly. Persisting textbuffer size, mousespeed. Allowing word wrap of textbuffer. (f491d3a39b)	CCTBX commit	Wed, 9 Feb 2022 01:05:15 +0000	93 lines
[git/cctbx_project] master: predueteration function (86968d5438)	CCTBX commit	Tue, 8 Feb 2022 12:08:12 -0800	156 lines
[git/cctbx_project] master: Fix sort that could compare objects (e9989f6ac6)	CCTBX commit	Tue, 8 Feb 2022 11:12:33 -0800	96 lines
[git/cctbx_project] master: CCTBXParser: clean up comment (a8cfab23d2)	CCTBX commit	Tue, 8 Feb 2022 10:55:29 -0800	94 lines
[git/dxtbx] main: FormatNXmx: open NeXus HDF5 files in SWMR mode (#478) (6fdca14f)	DXTBX commit	Tue, 8 Feb 2022 18:11:56 +0000	151 lines
[git/cctbx_project] master: Allow list of models to identify chain types from (still need to consolidate this) (6355fe49ec)	CCTBX commit	Tue, 8 Feb 2022 06:28:50 -0700	139 lines
[git/dxtbx] main: For dials/dials#1998 bring in UUID4 (#477) (42b19451)	DXTBX commit	Tue, 8 Feb 2022 10:31:28 +0000	309 lines
[git/cctbx_project] master: Update test for prepare_map_for_docking.py to include mask for ordered density. (b1a59408b5)	CCTBX commit	Tue, 8 Feb 2022 10:06:10 +0000	147 lines
[git/cctbx_project] master: Add comment about poor naming of local_standard_deviation_map, which returns local variance. (92886b8fed)	CCTBX commit	Tue, 8 Feb 2022 10:06:10 +0000	100 lines
[git/cctbx_project] master: Add method to find ordered density with Leslie/Abrahams local map variance. Report fraction of this ordered density remaining after cutting out sphere. Use fraction of cell volume occupied by ordered density to correct oversampling of FT for LLG calibration. This will probably make map LLG values half as large for significant scores as for crystallography, where typically only half the volume is occupied by ordered protein. (e867029ec5)	CCTBX commit	Tue, 8 Feb 2022 10:06:10 +0000	949 lines
[git/cctbx_project] master: temporary fix for dials/dials#1998 (#731) (47840f9b67)	CCTBX commit	Mon, 7 Feb 2022 14:25:51 -0500	143 lines
[git/dxtbx] main: DIALS 3.8.2 Changelog (456d981c)	DXTBX commit	Mon, 7 Feb 2022 18:18:37 +0000	155 lines
[git/cctbx_project] master: QI nprocs and Mopac H opt (d8fd07e82d)	CCTBX commit	Fri, 4 Feb 2022 13:51:30 -0800	185 lines
[git/cctbx_project] master: bootstrap: add kokkos-kernels (6cddaefbff)	CCTBX commit	Fri, 4 Feb 2022 12:30:50 -0800	143 lines
[git/cctbx_project] master: simtbx: build kokkos and kokkos-kernels dependencies with cmake (9f883a6366)	CCTBX commit	Fri, 4 Feb 2022 09:04:34 -0800	273 lines
[git/dxtbx] main: Fix dxtbx.plot_detector_models for matplotlib 3.5 (#476) (e65d0117)	DXTBX commit	Thu, 3 Feb 2022 16:02:54 +0000	228 lines
[git/cctbx_project] master: removed write restraints option (ea0e9ab993)	CCTBX commit	Wed, 2 Feb 2022 11:05:17 -0800	125 lines
[git/cctbx_project] master: detector_residuals plotting bugfix (b9e390221a)	CCTBX commit	Tue, 1 Feb 2022 15:02:59 -0800	110 lines
[git/cctbx_project] master: transfer torsion restraints and a start on writing restraints file (36254da923)	CCTBX commit	Tue, 1 Feb 2022 14:28:10 -0800	234 lines
[git/cctbx_project] master: CCTBXParser: --quiet flag still stores output (9b3505b834)	CCTBX commit	Tue, 1 Feb 2022 13:52:02 -0800	258 lines
[git/cctbx_project] master: CCTBXParser: add --quiet flag for suppressing output (13bb11cd87)	CCTBX commit	Tue, 1 Feb 2022 11:23:05 -0800	143 lines
[git/cctbx_project] tag 'v2022.1' created	CCTBX commit	Mon, 31 Jan 2022 23:21:21 -0800	40 lines
[git/cctbx_project] master: Update CHANGELOG.rst for 2022.1 release (1642971866)	CCTBX commit	Mon, 31 Jan 2022 23:21:21 -0800	96 lines
[git/cctbx_project] master: MOPAC is better with 1 THREAD and specific CHARGE (1c16af33b1)	CCTBX commit	Mon, 31 Jan 2022 18:00:01 -0800	127 lines

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February 2022

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