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February 2023

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Subject	From	Date	Size
[git/cctbx_project] master: Change map file to path (ff521ebf3d)	CCTBX commit	Tue, 28 Feb 2023 15:44:16 -0700	91 lines
[git/cctbx_project] tag 'v2023.2' created	CCTBX commit	Tue, 28 Feb 2023 12:56:06 -0800	40 lines
[git/cctbx_project] master: Update CHANGELOG.rst for 2023.2 release (0584c42ae2)	CCTBX commit	Tue, 28 Feb 2023 12:56:06 -0800	96 lines
[git/cctbx_project] master: bootstrap: restore no_boost_src default for CentOS 7 for Phenix builders (3d1c4e5089)	CCTBX commit	Tue, 28 Feb 2023 12:53:51 -0800	97 lines
[git/cctbx_project] master: Allow up to 625 columns in reflection_file_editor (a22eac30e7)	CCTBX commit	Mon, 27 Feb 2023 14:19:48 -0700	209 lines
[git/cctbx_project] master: Allow sending commands to chimerax (86d8467f0d)	CCTBX commit	Sun, 26 Feb 2023 08:30:09 -0700	99 lines
[git/cctbx_project] master: Use scale and icon_size for sizing icons to avoid oversized toolbar (d09dd0d71f)	CCTBX commit	Sat, 25 Feb 2023 21:24:54 +0000	129 lines
[git/cctbx_project] master: Keep sequences upper case; catch missing directories for lock (34bf4b1374)	CCTBX commit	Fri, 24 Feb 2023 13:18:05 -0700	174 lines
[git/cctbx_project] master: experiment_filter: add ability to exclude cells matching a cluster (#847) (a69c1a28a8)	CCTBX commit	Fri, 24 Feb 2023 11:14:28 -0500	182 lines
[git/cctbx_project] master: bootstrap: bump default Python to 3.7 (eb55696c23)	CCTBX commit	Fri, 24 Feb 2023 05:50:24 -0800	120 lines
[git/cctbx_project] master: bug fix for binning with resolution (2a0e5ada81)	CCTBX commit	Fri, 24 Feb 2023 12:55:12 +0000	207 lines
[git/cctbx_project] master: modify_cosym: remove experiments without a cb_op (#848) (36c99da305)	CCTBX commit	Thu, 23 Feb 2023 15:47:59 -0500	115 lines
[git/cctbx_project] master: Catch closed file and mismatch of matching segments (fcbdbc1639)	CCTBX commit	Wed, 22 Feb 2023 19:09:10 -0800	143 lines
[git/dxtbx] main: Ignore deprecated `pkg_resources.declare_namespace` warnings (#611) (17a0af34)	DXTBX commit	Wed, 22 Feb 2023 15:01:24 +0000	242 lines
[git/cctbx_project] master: Allow determining if ChimeraX is available (40ec3bf4ea)	CCTBX commit	Tue, 21 Feb 2023 15:52:40 -0700	302 lines
[git/cctbx_project] master: typo, try adjust lengths of rotation axes on top of each other to make their labels visible (3c0b392921)	CCTBX commit	Mon, 20 Feb 2023 20:05:11 +0000	176 lines
[git/cctbx_project] master: Tweak automated resolution choice to cope with full range of possibilities. (b92ca11e62)	CCTBX commit	Mon, 20 Feb 2023 12:14:45 +0000	191 lines
[git/cctbx_project] master: updated HBond plot pickles (3dbc4b882c)	CCTBX commit	Fri, 17 Feb 2023 13:32:51 -0800	74 lines
[git/cctbx_project] master: Change prepare_map_for_docking so that it makes a sensible guess for the d_min based on the voxel size, if a value isn't provided. The resolution seems unlikely to be higher than about 2.5 * the map spacing (with d_min/3 being a more likely spacing). (0e5ea79d63)	CCTBX commit	Fri, 17 Feb 2023 20:18:10 +0000	194 lines
[git/cctbx_project] master: bug fix for changing bin thresholds (f23603784d)	CCTBX commit	Fri, 17 Feb 2023 19:38:41 +0000	257 lines
[git/cctbx_project] master: conda: update Python version check to match environments (36de368099)	CCTBX commit	Thu, 16 Feb 2023 11:29:35 -0800	99 lines
[git/cctbx_project] master: bootstrap: update Python version check to match environments (ed7e0af011)	CCTBX commit	Thu, 16 Feb 2023 11:00:40 -0800	93 lines
[git/cctbx_project] master: Another convenience function with test. (d9375abcc9)	CCTBX commit	Thu, 16 Feb 2023 10:57:58 -0800	194 lines
[git/cctbx_project] master: conda: update Python version check to match environments (2212c6489c)	CCTBX commit	Thu, 16 Feb 2023 10:51:33 -0800	111 lines
[git/cctbx_project] master: bootstrap: consolidate Phenix builders (e689b6f555)	CCTBX commit	Thu, 16 Feb 2023 09:37:13 -0800	388 lines
[git/cctbx_project] master: Clean clutter (aef684b640)	CCTBX commit	Thu, 16 Feb 2023 09:15:06 -0800	158 lines
[git/cctbx_project] master: bug fix: ignore empty bins (bc56530c1b)	CCTBX commit	Thu, 16 Feb 2023 16:15:37 +0000	109 lines
[git/cctbx_project] master: better default value (1e0e52ba61)	CCTBX commit	Thu, 16 Feb 2023 10:11:02 +0000	148 lines
[git/cctbx_project] master: adjust axes width (78037466a8)	CCTBX commit	Thu, 16 Feb 2023 01:18:58 +0000	1243 lines
[git/cctbx_project] master: Create symmetry if necessary, temporarily remove the check (1b4d1b7a98)	CCTBX commit	Wed, 15 Feb 2023 17:04:21 -0800	112 lines
[git/cctbx_project] master: update (c2a6ad481e)	CCTBX commit	Tue, 14 Feb 2023 16:26:06 -0800	1382 lines
[git/cctbx_project] master: major reorg for more than just HIS... (644ef2895b)	CCTBX commit	Tue, 14 Feb 2023 16:24:40 -0800	1301 lines
[git/cctbx_project] master: Clean clutter (b0db0134d5)	CCTBX commit	Tue, 14 Feb 2023 12:00:30 -0800	61 lines
[git/cctbx_project] master: Allow turning on/off require_match_unit_cell_crystal_symmetry in box.py (3d6e3d8e62)	CCTBX commit	Tue, 14 Feb 2023 11:38:59 -0800	844 lines
[git/cctbx_project] master: bug fix: only make list of table column header names once (8471f3b41e)	CCTBX commit	Tue, 14 Feb 2023 16:04:08 +0000	122 lines
[git/cctbx_project] master: Avoid bug in setup_binner_d_star_sq_step, where there are sometimes low-resolution stragglers that aren't in any of the "used" bins. Easier to use setup_binner_d_star_sq_bin_size, which has a tolerance to avoid these stragglers. (22a4b90ec7)	CCTBX commit	Tue, 14 Feb 2023 09:57:07 +0000	245 lines
[git/cctbx_project] master: libtbx: set /DHAVE_SNPRINTF to avoid _snprintf compilation error (52a1dd359a)	CCTBX commit	Mon, 13 Feb 2023 17:34:19 -0800	105 lines
[git/cctbx_project] master: A better logic (5ccc12ecef)	CCTBX commit	Mon, 13 Feb 2023 14:04:41 -0800	200 lines
[git/cctbx_project] master: de-clutter (ee03204b21)	CCTBX commit	Mon, 13 Feb 2023 21:39:44 +0000	89 lines
[git/cctbx_project] master: more cosmetics (82b4d289ef)	CCTBX commit	Mon, 13 Feb 2023 21:16:39 +0000	2566 lines
[git/cctbx_project] master: GUI cosmetics (fc81fd477e)	CCTBX commit	Mon, 13 Feb 2023 18:26:44 +0000	74 lines
[git/cctbx_project] master: bug fix: ensure data labels are unique (f367cb376c)	CCTBX commit	Mon, 13 Feb 2023 14:28:32 +0000	175 lines
[git/cctbx_project] master: Improve numerical stability of map signal and noise analysis. Expand ordered volume mask slightly. (1e6654271b)	CCTBX commit	Mon, 13 Feb 2023 10:18:57 +0000	694 lines
[git/cctbx_project] master: Allow adding binned reflections with opacity=1 as a new dataset (5658da27f4)	CCTBX commit	Sun, 12 Feb 2023 20:31:42 +0000	2100 lines
[git/cctbx_project] master: Ensure miller_array_operation is reset after new command. Tooltip on preset button. (6ebab4d1fb)	CCTBX commit	Sun, 12 Feb 2023 00:47:25 +0000	632 lines
[git/cctbx_project] master: Make post_query usable as standalone function. With tests. (9b258ad714)	CCTBX commit	Fri, 10 Feb 2023 16:58:40 -0800	347 lines
[git/cctbx_project] master: Show actual datalabels of datasets involved beneath each preset-button. (15c5598aa7)	CCTBX commit	Fri, 10 Feb 2023 17:49:16 +0000	424 lines
[git/cctbx_project] master: added restraints to hBond (45fb3017a4)	CCTBX commit	Thu, 9 Feb 2023 15:25:43 -0800	376 lines
[git/cctbx_project] master: Use current suffixes in example (0130c41449)	CCTBX commit	Thu, 9 Feb 2023 10:46:54 -0800	95 lines
[git/cctbx_project] master: comment out button in default_user_preset_buttons.py (3f9b2a6f12)	CCTBX commit	Thu, 9 Feb 2023 17:41:21 +0000	176 lines
[git/cctbx_project] master: Add button for creating miller array with INFO>0.2 and I/SigI<0.5 (8e5a1ac1e0)	CCTBX commit	Thu, 9 Feb 2023 17:15:23 +0000	373 lines
[git/cctbx_project] master: Minor tweak to the way minimum sigmaE is set. (4088c8f7df)	CCTBX commit	Thu, 9 Feb 2023 10:03:06 +0000	123 lines
[git/cctbx_project] master: Utility for merging models. (7e62e028bb)	CCTBX commit	Wed, 8 Feb 2023 15:33:53 -0800	892 lines
[git/cctbx_project] master: added rotamer info for original and alternatives (a49a202cd9)	CCTBX commit	Wed, 8 Feb 2023 13:49:08 -0800	377 lines
[git/cctbx_project] master: update (7bdd576059)	CCTBX commit	Tue, 7 Feb 2023 18:20:21 -0800	87 lines
[git/cctbx_project] master: update (77362fe3ff)	CCTBX commit	Tue, 7 Feb 2023 17:35:43 -0800	99 lines
[git/cctbx_project] master: file 2 open (02b6000dda)	CCTBX commit	Tue, 7 Feb 2023 17:00:48 -0800	194 lines
[git/cctbx_project] master: big changes to HIS protonation options (ee6de3b183)	CCTBX commit	Tue, 7 Feb 2023 16:57:11 -0800	1894 lines
[git/cctbx_project] master: MNT: switch deprecated std::sprintf to std::snprintf (b6e323ebcd)	CCTBX commit	Tue, 7 Feb 2023 14:30:05 -0800	1710 lines
[git/cctbx_project] master: In auto_sharpen_isotropic, weight resolution bins by FSC. (cd7b925298)	CCTBX commit	Tue, 7 Feb 2023 14:13:41 +0000	126 lines
[git/cctbx_project] master: Add new auto_sharpen_by_FSC method, which is bin-wise instead of modelling the resolution dependence purely through a B-factor. It didn't work as well as auto_sharpen_isotropic so not used, but might be worth reinvestigating if bin-wise were replaced by a smooth function of resolution, like a spline fit. (e44810aa58)	CCTBX commit	Tue, 7 Feb 2023 10:13:52 +0000	191 lines
[git/cctbx_project] master: clean clutter (6a215fbc53)	CCTBX commit	Mon, 6 Feb 2023 08:59:45 -0800	123 lines
[git/cctbx_project] master: Do not shift model if just a dummy map_manager (083310f1ae)	CCTBX commit	Sun, 5 Feb 2023 16:22:19 -0800	94 lines
[git/cctbx_project] master: Add method to transfer symmetry and shift_cart from one model to another (c2fd8b94c2)	CCTBX commit	Sun, 5 Feb 2023 17:03:37 -0700	297 lines
[git/cctbx_project] master: Revert change allowing multiple models to create fmodel (dd606c0e0c)	CCTBX commit	Sat, 4 Feb 2023 12:38:23 -0700	99 lines
[git/cctbx_project] master: Allow multiple models in data_manager to generate fmodel (40e0403cd0)	CCTBX commit	Sat, 4 Feb 2023 09:31:02 -0700	140 lines
[git/cctbx_project] master: Fix typo (6210883adf)	CCTBX commit	Sat, 4 Feb 2023 08:43:36 -0700	87 lines
[git/cctbx_project] master: Add capability to merge additional models into model object (b55baeb034)	CCTBX commit	Sat, 4 Feb 2023 08:30:59 -0700	305 lines
[git/cctbx_project] master: added water bonds to .pml file (d7e9e29781)	CCTBX commit	Fri, 3 Feb 2023 13:38:15 -0800	238 lines
[git/cctbx_project] master: added ADP Z scores to model and model stats (8a42ee9697)	CCTBX commit	Fri, 3 Feb 2023 13:37:19 -0800	201 lines
[git/cctbx_project] master: basics - addition of ADP Z scores via flex array (8d4d0e2271)	CCTBX commit	Fri, 3 Feb 2023 13:36:14 -0800	111 lines
[git/cctbx_project] master: Change ordered volume calculation to just use local map variance. It turns out that local difference map variance is not very stable and makes the results worse. (514f7d15b4)	CCTBX commit	Fri, 3 Feb 2023 15:21:27 +0000	251 lines
[git/cctbx_project] master: try catch block (6ab3130bfd)	CCTBX commit	Fri, 3 Feb 2023 13:49:46 +0000	299 lines
[git/cctbx_project] master: Authors' ORCIDs for mmCIF output. New categories in sorting. (4be4ad87e5)	CCTBX commit	Thu, 2 Feb 2023 16:38:08 -0800	236 lines
[git/cctbx_project] master: Small cleanup of imports (bc347dfc19)	CCTBX commit	Thu, 2 Feb 2023 11:45:40 -0800	354 lines
[git/cctbx_project] master: bug fix (f2a7bd98c6)	CCTBX commit	Thu, 2 Feb 2023 14:25:50 +0000	145 lines
[git/cctbx_project] master: Plot skew-kurtosis plot in hbond tool. (6d7f8805ae)	CCTBX commit	Wed, 1 Feb 2023 16:24:32 -0800	465 lines
[git/cctbx_project] master: Data and filtering procedure for hbond utility. (e6a0f60150)	CCTBX commit	Wed, 1 Feb 2023 14:27:41 -0800	280 lines
[git/cctbx_project] master: better default values for sigmas size (2aef8fe8a5)	CCTBX commit	Wed, 1 Feb 2023 18:33:37 +0000	128 lines
[git/cctbx_project] master: updates (06cbd74ce3)	CCTBX commit	Wed, 1 Feb 2023 10:17:13 -0800	91 lines
[git/cctbx_project] master: bug fix (b6614962d7)	CCTBX commit	Wed, 1 Feb 2023 16:15:17 +0000	92 lines
[git/cctbx_project] master: print helpful error message when supplying wrong file path (f88e0caafc)	CCTBX commit	Wed, 1 Feb 2023 11:39:12 +0000	131 lines
[git/cctbx_project] master: Update CHANGELOG.rst for 2023.1 release (7a8b832daf)	CCTBX commit	Tue, 31 Jan 2023 18:20:32 -0800	94 lines
[git/cctbx_project] tag 'v2023.1' created	CCTBX commit	Tue, 31 Jan 2023 18:20:32 -0800	40 lines

CCTBX-COMMIT Archives

February 2023

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