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July 2018

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Subject	From	Date	Size
[git/cctbx] master: update GUI values for chain_comparison (b20993cec)	CCTBX commit	Mon, 30 Jul 2018 17:28:34 -0600	152 lines
[git/cctbx] master: Correct comment and docstring (7372898d3)	CCTBX commit	Mon, 30 Jul 2018 11:48:20 +0100	123 lines
[git/cctbx] master: minor fix for case where autosharpen has not scaled anything (0edeb35a1)	CCTBX commit	Sat, 28 Jul 2018 15:12:58 -0600	427 lines
[git/cctbx] master: Ensure thickness and material are recorded in the detector model (4a6ba8177)	CCTBX commit	Fri, 27 Jul 2018 11:29:46 +0100	109 lines
[git/cctbx] master: It appears 'mu' was never being set in the panel (805d868b2)	CCTBX commit	Fri, 27 Jul 2018 11:17:55 +0100	81 lines
Jenkins CCTBX Branch Tests branch origin/dxtbx-sacla Unstable	DLS Jenkins	Fri, 27 Jul 2018 11:07:22 +0100	46 lines
[git/cctbx] master: Better handle check_format=False in ImageSetLazy. Fixes dials/dials#601. (70f973612)	CCTBX commit	Thu, 26 Jul 2018 15:33:41 -0700	226 lines
[git/cctbx] master: Chain-comparison now returns object with method show_summary() (cbb1e05e2)	CCTBX commit	Thu, 26 Jul 2018 13:12:37 -0600	230 lines
[git/cctbx] master: Tidy up output for RSR integration (2d6c9bb9a)	CCTBX commit	Wed, 25 Jul 2018 18:25:28 -0700	963 lines
[git/cctbx] master: make sure master_sel is updated, because RSR messes with ncs_groups on its own. (31f0dab8b)	CCTBX commit	Wed, 25 Jul 2018 15:21:50 -0700	86 lines
[git/cctbx] master: chain_comparison: add parameters for GUI (699f137b4)	CCTBX commit	Wed, 25 Jul 2018 13:21:26 -0700	114 lines
[git/cctbx] master: dxtbx class for Rayonix MX300-HS converted into HDF5 by Cheetah pipeline at SACLA (dc1716583)	CCTBX commit	Thu, 26 Jul 2018 04:08:24 +0900	358 lines
[git/cctbx] master: dxtbx class for Rayonix in SACLA: improved understand() (5c7416bcd)	CCTBX commit	Thu, 26 Jul 2018 04:08:24 +0900	106 lines
[git/cctbx] master: dxtbx class for SACLA MPCCD: supported Phase III MPCCD and compact MPCCD (62cb0dd33)	CCTBX commit	Thu, 26 Jul 2018 04:08:24 +0900	464 lines
[git/cctbx] master: CCTBXParser: check for None before checking path (339307fae)	CCTBX commit	Tue, 24 Jul 2018 18:16:49 -0700	103 lines
[git/cctbx] master: remove blanks (6b32a03a6)	CCTBX commit	Tue, 24 Jul 2018 17:41:09 -0600	59 lines
[git/cctbx] master: MI:bugfix in using rotamer fitting (05c5c5f8e)	CCTBX commit	Tue, 24 Jul 2018 15:26:58 -0700	231 lines
Jenkins CCTBX Branch Tests branch origin/dxtbx-sacla Still Unstable	DLS Jenkins	Tue, 24 Jul 2018 23:11:26 +0100	50 lines
Jenkins CCTBX Branch Tests branch origin/dxtbx-sacla Unstable	DLS Jenkins	Tue, 24 Jul 2018 23:08:25 +0100	47 lines
[git/cctbx] master: Table one: add options for twinning (e38092722)	CCTBX commit	Tue, 24 Jul 2018 09:19:26 -0700	139 lines
[git/cctbx] master: Add capability for non-proper ncs in map_symmetry (4c294825b)	CCTBX commit	Mon, 23 Jul 2018 17:43:15 -0600	89 lines
[git/cctbx] master: Add capability for non-proper ncs in map_symmetry (d1e0daece)	CCTBX commit	Mon, 23 Jul 2018 17:39:52 -0600	279 lines
[git/cctbx] master: MolProbity: enable input for twin law (867dcb6ec)	CCTBX commit	Mon, 23 Jul 2018 15:36:30 -0700	196 lines
[git/cctbx] master: Add automation for sequence_from_map (a50979428)	CCTBX commit	Sun, 22 Jul 2018 18:53:43 -0700	206 lines
[git/cctbx] master: Set scale_max=99999 for map_to_structure_factors and map_box and allow user to set it (75ccbe0ac)	CCTBX commit	Sun, 22 Jul 2018 11:33:31 -0700	215 lines
[git/cctbx] master: Make map/model shifts available (8bbdd589d)	CCTBX commit	Fri, 20 Jul 2018 17:08:08 -0700	233 lines
[git/cctbx] master: add score (23629c676)	CCTBX commit	Fri, 20 Jul 2018 15:54:55 -0600	104 lines
[git/cctbx] master: fix bug where include_helical_symmetry=true (42cabe386)	CCTBX commit	Fri, 20 Jul 2018 15:17:49 -0600	88 lines
[git/cctbx] master: catch case of no ncs info (4476415a9)	CCTBX commit	Fri, 20 Jul 2018 10:25:52 -0600	85 lines
[git/cctbx] master: fix result if no ncs (f23b18c2b)	CCTBX commit	Thu, 19 Jul 2018 14:22:57 -0700	131 lines
[git/cctbx] master: start passing selection, with test (275031b68)	CCTBX commit	Thu, 19 Jul 2018 11:27:41 -0700	857 lines
[git/cctbx] master: Attempt to put hydrogens on the model (aeaacc8c7)	CCTBX commit	Thu, 19 Jul 2018 11:27:40 -0700	201 lines
[git/cctbx] master: Map to the asymmetric unit while loading data and add a sort after the data is loaded (eecf92693)	CCTBX commit	Wed, 18 Jul 2018 16:37:54 -0700	170 lines
[git/cctbx] master: Bugfix for cluster.unit_cell. Fixes #221 (4119fbedb)	CCTBX commit	Wed, 18 Jul 2018 15:31:13 -0700	119 lines
[git/cctbx] master: Merge branch 'condenced_clashscore' (f88b902e2)	CCTBX commit	Wed, 18 Jul 2018 14:52:34 -0700	67 lines
[git/cctbx] master: Changing tests to adopt latest changes - skippin so lines (bd81b67a4)	CCTBX commit	Wed, 18 Jul 2018 14:47:10 -0700	283 lines
[git/cctbx] master: Add data reading to prototype merging app (6046eb370)	CCTBX commit	Wed, 18 Jul 2018 14:33:56 -0700	352 lines
[git/cctbx] master: Hold on to full_crystal_symmetry and grid (851593047)	CCTBX commit	Wed, 18 Jul 2018 14:26:29 -0600	305 lines
[git/cctbx] master: Minor typo (d01ccb2ea)	CCTBX commit	Wed, 18 Jul 2018 13:03:34 -0600	87 lines
[git/cctbx] master: Allow symmetry mismatch in map_box (b6edbf230)	CCTBX commit	Wed, 18 Jul 2018 13:00:07 -0600	207 lines
[git/cctbx] master: Merge branch 'master' into condenced_clashscore (819b2c7ce)	CCTBX commit	Wed, 18 Jul 2018 11:22:27 -0700	203 lines
[git/cctbx] master: fix ignore_symmetry_conflicts (ff075a641)	CCTBX commit	Wed, 18 Jul 2018 08:55:20 -0700	141 lines
[git/cctbx] master: Allow partial maps in segment_and_split_map (b7d2ddafe)	CCTBX commit	Wed, 18 Jul 2018 08:59:52 -0600	369 lines
[git/cctbx] master: make error message slightly more useful (5e963e2b7)	CCTBX commit	Wed, 18 Jul 2018 08:04:45 +0100	87 lines
[git/cctbx] master: Activate test. (34fcf98b7)	CCTBX commit	Tue, 17 Jul 2018 17:58:08 -0700	79 lines
[git/cctbx] master: Make neutralize_scatterers available in pdbtools. (4d734e2d5)	CCTBX commit	Tue, 17 Jul 2018 16:53:12 -0700	350 lines
[git/cctbx] master: removed another so contact check (8e8a9d77e)	CCTBX commit	Tue, 17 Jul 2018 18:00:02 -0400	85 lines
[git/cctbx] master: Allow user to keep low density or not in extract_unique (86bd33684)	CCTBX commit	Tue, 17 Jul 2018 14:53:01 -0700	194 lines
[git/cctbx] master: Make sure that restraints manager will use updated vdw radii after neutralization. (88553b57d)	CCTBX commit	Tue, 17 Jul 2018 13:39:50 -0700	2563 lines
[git/cctbx] master: Make sure that restraints manager is dropped when calling neutralize_scatterers. Make sure that pdb_hierarchy also contains neutral atoms. (6a81a55c6)	CCTBX commit	Tue, 17 Jul 2018 12:09:53 -0700	169 lines
[git/cctbx] master: added DVT to ideal ligands (4dd63f0f6)	CCTBX commit	Tue, 17 Jul 2018 11:51:17 -0700	114 lines
[git/cctbx] master: Add neutralize_scatterers function to model class. Plus test. (4aa2227b9)	CCTBX commit	Tue, 17 Jul 2018 11:18:36 -0700	1345 lines
[git/cctbx] master: Check rotamer outliers for early exit (87574fd43)	CCTBX commit	Tue, 17 Jul 2018 11:16:11 -0700	93 lines
[git/cctbx] master: clashscore will ignore 'so' contact lines (561300a4f)	CCTBX commit	Tue, 17 Jul 2018 12:43:59 -0400	87 lines
[git/cctbx] master: Retain original stack trace (43914c50c)	CCTBX commit	Tue, 17 Jul 2018 09:35:16 +0100	117 lines
[git/cctbx] master: Add ignore_symmetry_conflicts (646e17f8d)	CCTBX commit	Mon, 16 Jul 2018 17:35:40 -0700	104 lines
[git/cctbx] master: Moved to phenix and now uses program template (4bb80cbb1)	CCTBX commit	Mon, 16 Jul 2018 17:00:32 -0700	947 lines
[git/cctbx] master: Move histogram function to here (5aec2b664)	CCTBX commit	Mon, 16 Jul 2018 17:00:32 -0700	154 lines
[git/cctbx] master: Stop with a sorry instead of crash when there are atoms without scattering factors. (d38484999)	CCTBX commit	Mon, 16 Jul 2018 16:32:44 -0700	167 lines
[git/cctbx] master: Add GUI phil for map_to_structure_factors (57694d115)	CCTBX commit	Mon, 16 Jul 2018 15:12:02 -0700	104 lines
[git/cctbx] master: Fix failure to initialize original_crystal_symmetry when running from mtz (cb1480f9d)	CCTBX commit	Mon, 16 Jul 2018 14:51:56 -0600	87 lines
[git/cctbx] master: Test psana2 interface. (e2e384a52)	CCTBX commit	Mon, 16 Jul 2018 13:23:12 -0700	417 lines
[git/cctbx] master: Use detector object from psana to obtain calib files. (2686deac9)	CCTBX commit	Mon, 16 Jul 2018 13:23:12 -0700	370 lines
[git/cctbx] master: Read calibration from env variable. (e6103a4fe)	CCTBX commit	Mon, 16 Jul 2018 13:23:12 -0700	159 lines
[git/cctbx] master: Add version checking for psana2. (aa139d19f)	CCTBX commit	Mon, 16 Jul 2018 13:23:12 -0700	445 lines
[git/cctbx] master: Clean clutter. (68805a0da)	CCTBX commit	Mon, 16 Jul 2018 13:23:12 -0700	60 lines
[git/cctbx] master: Add random-sequence tool (e739a0713)	CCTBX commit	Sun, 15 Jul 2018 20:52:57 -0600	166 lines
[git/cctbx] master: disable tolerance check -- this test is unstable (works on my mac, fails on anaconda). (b7bec6fa0)	CCTBX commit	Sun, 15 Jul 2018 19:11:43 -0700	105 lines
[git/cctbx] master: More fixes from t96. (88d29fee7)	CCTBX commit	Sun, 15 Jul 2018 18:49:38 -0700	292 lines
[git/cctbx] master: Work-around for OXT (5a122e2e4)	CCTBX commit	Sun, 15 Jul 2018 17:26:12 -0700	210 lines
[git/cctbx] master: Bugs uncovered by t96 (1571dc85f)	CCTBX commit	Sun, 15 Jul 2018 16:58:45 -0700	120 lines
[git/cctbx] master: 2nd part of: Make rotamer fitting use per-atom vdW radii from ener_lib.cif to evaluate clashes. Enable fititng with H atoms. Numerous bugfixes. Reduce redundancy in setting up tests. Improve thoroughness of existing tests and add more new tests. (02d36f827)	CCTBX commit	Sun, 15 Jul 2018 16:28:10 -0700	84 lines
[git/cctbx] master: Removed as nonsensical (f63de827e)	CCTBX commit	Sun, 15 Jul 2018 16:28:10 -0700	456 lines
[git/cctbx] master: 3rd part of: Make rotamer fitting use per-atom vdW radii from ener_lib.cif to evaluate clashes. Enable fititng with H atoms. Numerous bugfixes. Reduce redundancy in setting up tests. Improve thoroughness of existing tests and add more new tests. (c943361b0)	CCTBX commit	Sun, 15 Jul 2018 16:28:10 -0700	911 lines
[git/cctbx] master: Make rotamer fitting use per-atom vdW radii from ener_lib.cif to evaluate clashes. Enable fititng with H atoms. Numerous bugfixes. Reduce redundancy in setting up tests. Improve thoroughness of existing tests and add more new tests. (7cd6b9c81)	CCTBX commit	Sun, 15 Jul 2018 16:28:10 -0700	105 lines
[git/cctbx] master: Remove previous code (43e8ec95e)	CCTBX commit	Fri, 13 Jul 2018 10:34:19 -0700	183 lines
[git/cctbx] master: model manager: add parameter for fast_clash in clashscore calculation (a6f49aaaa)	CCTBX commit	Thu, 12 Jul 2018 21:00:55 -0700	106 lines
[git/cctbx] master: Fix tests to adopt changes in clashscore calculations (e7de394fb)	CCTBX commit	Thu, 12 Jul 2018 17:57:15 -0700	346 lines
[git/cctbx] master: correctly parse the line (68c698670)	CCTBX commit	Thu, 12 Jul 2018 17:14:47 -0700	170 lines
[git/cctbx] master: Switching fast part to CONdensed output (85268f9c1)	CCTBX commit	Thu, 12 Jul 2018 16:43:48 -0700	235 lines
[git/cctbx] master: Changing slow part to CONdensed output (388ef5f89)	CCTBX commit	Thu, 12 Jul 2018 16:43:23 -0700	243 lines
[git/cctbx] master: Bugfix: pring messages appropriately, not always the same. (f753d1e24)	CCTBX commit	Thu, 12 Jul 2018 15:53:33 -0700	123 lines
[git/cctbx] master: run_program: add argument for custom_process_arguments (ba4653cd8)	CCTBX commit	Thu, 12 Jul 2018 15:06:59 -0700	160 lines
[git/cctbx] master: Fix spelling error in caption. (da93c4cef)	CCTBX commit	Thu, 12 Jul 2018 09:09:16 +0100	86 lines
[git/cctbx] master: Remove debugging code (0fe22f15a)	CCTBX commit	Wed, 11 Jul 2018 19:56:38 -0700	237 lines
[git/cctbx] master: Fast mode for clashscore calculations. By default in RSR (f1819f4b9)	CCTBX commit	Wed, 11 Jul 2018 18:29:42 -0700	866 lines
[git/cctbx] master: assorted bugfixes (91e6f6258)	CCTBX commit	Wed, 11 Jul 2018 15:19:33 -0700	982 lines
[git/cctbx] master: Remove deprecated functionality (652d85d02)	CCTBX commit	Mon, 9 Jul 2018 14:41:15 -0700	295 lines
[git/cctbx] master: bugfix, updated tests. (653a454b6)	CCTBX commit	Mon, 9 Jul 2018 11:16:15 -0700	306 lines
[git/cctbx] master: speed up find_ss_from_ca for cases where there is NCS (90c0ac150)	CCTBX commit	Mon, 9 Jul 2018 10:56:11 -0700	78 lines
[git/cctbx] master: Fix mistake in extract_map_and_model write_ccp4_map (cc2a7b677)	CCTBX commit	Sat, 7 Jul 2018 15:30:43 -0600	89 lines
[git/cctbx] master: Do something if point is outside map (d4913a97e)	CCTBX commit	Sat, 7 Jul 2018 06:01:06 -0700	103 lines
[git/cctbx] master: stub for new merging application. run libtbx.python phil.py (7f1a44e3b)	CCTBX commit	Fri, 6 Jul 2018 21:19:37 -0700	1297 lines
[git/cctbx] master: Getting rid of another .index(). Early exit. Faster SS generation. (d8446a798)	CCTBX commit	Fri, 6 Jul 2018 17:32:28 -0700	160 lines
[git/cctbx] master: Getting rid of slow index by wasting some memory. 6x faster for 20k bonds. (86b15571f)	CCTBX commit	Fri, 6 Jul 2018 17:32:28 -0700	103 lines
[git/cctbx] master: First touch to speed up SS restraints. This func is now 10x faster (d647f952f)	CCTBX commit	Fri, 6 Jul 2018 17:32:28 -0700	122 lines
[git/cctbx] master: Allow choice of wrapping/not wrapping in superpose_maps (f4636bbec)	CCTBX commit	Fri, 6 Jul 2018 12:23:03 -0700	181 lines
[git/cctbx] master: Adapt code to changes in write_ccp4_map method of extract_box_around_model_and_map. (c8767224c)	CCTBX commit	Thu, 5 Jul 2018 16:23:53 -0700	154 lines
[git/cctbx] master: bugfix (087b00f63)	CCTBX commit	Thu, 5 Jul 2018 15:18:06 -0700	93 lines
[git/cctbx] master: Parameter for more relaxed acceptance. Don't fail on error. (b26eecd9e)	CCTBX commit	Thu, 5 Jul 2018 15:18:06 -0700	254 lines
Jenkins CCTBX Branch Tests branch origin/reworked_fast_lstbx Failure	DLS Jenkins	Thu, 5 Jul 2018 12:41:11 +0100	1057 lines
[git/cctbx] master: Allow user to set threshold for density_select in auto_sharpen (476535b08)	CCTBX commit	Wed, 4 Jul 2018 20:27:10 -0700	274 lines
[git/cctbx] master: write out original unit cell grid and crystal symmetry (8d4d98266)	CCTBX commit	Wed, 4 Jul 2018 15:03:30 -0700	319 lines
[git/cctbx] master: Update to allow using original_crystal_symmetry and grid (fab2c32a2)	CCTBX commit	Wed, 4 Jul 2018 14:22:15 -0700	659 lines
[git/cctbx] master: fix detector panel identifier pickling bug (75a9dc079)	CCTBX commit	Wed, 4 Jul 2018 14:51:03 +0100	149 lines
[git/cctbx] master: fix float/double for resolve (68e16a06e)	CCTBX commit	Tue, 3 Jul 2018 16:45:38 -0700	113 lines
[git/cctbx] master: tracker bugfix (05e931fef)	CCTBX commit	Tue, 3 Jul 2018 16:40:24 -0700	91 lines
[git/cctbx] master: return as double (b9d100841)	CCTBX commit	Tue, 3 Jul 2018 16:30:50 -0600	87 lines
[git/cctbx] master: fix offset problem (ee9d68efd)	CCTBX commit	Tue, 3 Jul 2018 15:49:01 -0600	127 lines
Jenkins 5b cctbx MacOS build 2742 Fixed	DLS Jenkins	Tue, 3 Jul 2018 21:06:57 +0100	43 lines
Jenkins 5a cctbx Tests build 6890 Fixed	DLS Jenkins	Tue, 3 Jul 2018 20:53:39 +0100	42 lines
[git/cctbx] master: One more move (7b617d52c)	CCTBX commit	Tue, 3 Jul 2018 12:47:06 -0700	159 lines
[git/cctbx] master: Move test (879f1fa18)	CCTBX commit	Tue, 3 Jul 2018 12:46:22 -0700	159 lines
[git/cctbx] master: Move test to mmtbx. (fa61e7481)	CCTBX commit	Tue, 3 Jul 2018 12:45:49 -0700	108 lines
Jenkins 5b cctbx MacOS build 2741 Unstable	DLS Jenkins	Tue, 3 Jul 2018 19:19:54 +0100	53 lines
[git/cctbx] master: write out original gridding afer auto_sharpen (684f59852)	CCTBX commit	Tue, 3 Jul 2018 12:03:45 -0600	456 lines
Jenkins 5a cctbx Tests build 6888 Unstable	DLS Jenkins	Tue, 3 Jul 2018 18:29:19 +0100	51 lines
[git/cctbx] master: Add test. (bb715c5fe)	CCTBX commit	Tue, 3 Jul 2018 10:24:22 -0700	184 lines
[git/cctbx] master: Bugfix: dont use values of previously used scatt table when setting up scattering type registry. (009140d30)	CCTBX commit	Tue, 3 Jul 2018 10:10:25 -0700	91 lines
[git/cctbx] master: Remove restriction that input map be full unit cell (cb0dd5795)	CCTBX commit	Tue, 3 Jul 2018 10:47:49 -0600	283 lines
[git/cctbx] master: Moving point-group symmetry from segment_and_split_map to ncs.py (03b8847e3)	CCTBX commit	Tue, 3 Jul 2018 09:59:43 -0600	73 lines
[git/cctbx] master: Clean up new test linter and clutter warnings (492b24b6d)	CCTBX commit	Tue, 3 Jul 2018 15:11:28 +0100	482 lines
[git/cctbx] master: dxtbx: Add pytest option '--regression' (421475f73)	CCTBX commit	Tue, 3 Jul 2018 14:13:58 +0100	112 lines
[git/cctbx] master: rename test file to accurately describe contents (f460f5cbd)	CCTBX commit	Tue, 3 Jul 2018 14:01:37 +0100	160 lines
[git/cctbx] master: Merge image reading tests with dials_regression (edf34ccbe)	CCTBX commit	Tue, 3 Jul 2018 13:51:27 +0100	861 lines
[git/cctbx] master: fix for generic_flex_image call (83675b7de)	CCTBX commit	Tue, 3 Jul 2018 09:40:15 +0100	86 lines
[git/cctbx] master: Do minimization even when ncs is present (5ed668448)	CCTBX commit	Mon, 2 Jul 2018 11:24:24 -0700	94 lines
[git/cctbx] master: support for binning in generic_flex_image (0ad4f68e7)	CCTBX commit	Mon, 2 Jul 2018 16:31:07 +0100	317 lines
[git/cctbx] master: Set minimum similarity for getting unique part of moleculeto 99% from 90% so that duplicate chains with different lengths as in emd_6000 are counted as different. (220a86dfd)	CCTBX commit	Sun, 1 Jul 2018 14:03:49 -0700	107 lines

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July 2018

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