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Subject	From	Date	Size
[git/cctbx] master: First version of documentation for F to G conversion, referred to in section B.3 of the Waterman (2016) paper. (3b2081b05)	CCTBX commit	Fri, 29 Dec 2017 21:18:37 -0800	472 lines
Jenkins 5a cctbx Tests build 5644 Fixed	DLS Jenkins	Sat, 23 Dec 2017 23:01:25 +0000	37 lines
[git/cctbx] master: clean clutter (cd1c6b778)	CCTBX commit	Sat, 23 Dec 2017 15:55:08 -0700	48 lines
Jenkins 5a cctbx Tests build 5643 Unstable	DLS Jenkins	Sat, 23 Dec 2017 22:49:22 +0000	34 lines
[git/cctbx] master: Make default ncs helical tolerances match find_ncs.py (e7bbebb1a)	CCTBX commit	Sat, 23 Dec 2017 14:43:15 -0800	268 lines
[git/cctbx] master: Update tests (bc318f24d)	CCTBX commit	Fri, 22 Dec 2017 19:28:45 -0800	84 lines
[git/cctbx] master: Catch case where sequence is protein but listed as AAAAAAAAAAAAA (28b27a457)	CCTBX commit	Fri, 22 Dec 2017 19:14:02 -0800	261 lines
[git/cctbx] master: The nanoBragg class function to_smv_format() has been ported to Python. This allows considerably more flexibility. Options are added to write the rotation matrix to the SMV header, as well as a user-defined string with extra information, and also to write gz-compressed SMV files readable by DIALS. (7b63622a9)	CCTBX commit	Thu, 21 Dec 2017 16:39:21 -0800	609 lines
[git/cctbx] master: Including the definition of default_buffer_size in more than one object file appears to preclude linkage of the objects together. Instead, define it only where it is needed in meta_ext.cpp. (2d93efd55)	CCTBX commit	Thu, 21 Dec 2017 16:39:21 -0800	110 lines
[git/cctbx] master: 12% pdb_interpretation speedup (4677c2fd7)	CCTBX commit	Thu, 21 Dec 2017 16:36:11 -0800	848 lines
[git/cctbx] master: clean clutter (38dccddb9)	CCTBX commit	Thu, 21 Dec 2017 14:07:16 -0800	48 lines
[git/cctbx] master: Allow segment_and_split_map to recognize that unit cell has changed in map_box (57ae5ecf2)	CCTBX commit	Thu, 21 Dec 2017 13:55:55 -0800	233 lines
[git/cctbx] master: Add OK (b6df48a6c)	CCTBX commit	Wed, 20 Dec 2017 16:02:41 -0800	92 lines
[git/cctbx] master: Fix typo (e2375805d)	CCTBX commit	Wed, 20 Dec 2017 16:00:47 -0800	80 lines
Jenkins 5a cctbx Tests build 5630 Fixed	DLS Jenkins	Wed, 20 Dec 2017 18:45:08 +0000	36 lines
[git/cctbx] master: decide on whether to use points outside cell based on use_sg_symmetry (09f082d1d)	CCTBX commit	Wed, 20 Dec 2017 10:44:45 -0800	94 lines
[git/cctbx] master: Use .crystal_symmetry() method of map reader. Fix test. (c02d40154)	CCTBX commit	Wed, 20 Dec 2017 10:39:27 -0800	129 lines
[git/cctbx] master: Set defaults. (d0f707ace)	CCTBX commit	Wed, 20 Dec 2017 09:53:26 -0800	147 lines
Jenkins 5a cctbx Tests build 5628 Unstable	DLS Jenkins	Wed, 20 Dec 2017 17:50:01 +0000	34 lines
[git/cctbx] master: Add three options to compute RSR gradients. (a0132ccb4)	CCTBX commit	Wed, 20 Dec 2017 09:40:00 -0800	826 lines
[git/cctbx] master: Work-around for a bad map file that contains inconsistent box information. (1e452f911)	CCTBX commit	Wed, 20 Dec 2017 06:01:53 -0800	100 lines
[git/cctbx] master: Test for remove_residue_groups_with_atoms_on_special_positions_selective (e6b662a1e)	CCTBX commit	Wed, 20 Dec 2017 06:01:53 -0800	218 lines
[git/cctbx] master: fix typo (7c88f41f9)	CCTBX commit	Tue, 19 Dec 2017 15:23:50 -0800	77 lines
[git/cctbx] master: clean clutter (9800199f8)	CCTBX commit	Tue, 19 Dec 2017 14:14:00 -0800	67 lines
[git/cctbx] master: clean clutter (6973ff3b9)	CCTBX commit	Tue, 19 Dec 2017 14:13:14 -0800	48 lines
[git/cctbx] master: clean clutter (97c3be07a)	CCTBX commit	Tue, 19 Dec 2017 14:12:38 -0800	48 lines
[git/cctbx] master: Update ncs copies with helical ops in segment_and_split (f78f8422b)	CCTBX commit	Tue, 19 Dec 2017 15:02:44 -0700	80 lines
[git/cctbx] master: remove ?? from sequence and fix output (d6f5b2658)	CCTBX commit	Tue, 19 Dec 2017 12:32:43 -0800	92 lines
[git/cctbx] master: Be sure to be able to get au if necessary (15556b5b6)	CCTBX commit	Tue, 19 Dec 2017 12:18:07 -0800	380 lines
[git/cctbx] master: make sequence reading consistent (2fb0d43f7)	CCTBX commit	Tue, 19 Dec 2017 08:38:27 -0800	257 lines
[git/cctbx] master: minor printout change (51a5f49b2)	CCTBX commit	Tue, 19 Dec 2017 07:50:24 -0800	70 lines
[git/cctbx] master: Allow chain groupings like AAB in extract_unique_part_of_hierarchy and extract_unique_part_of_sequences (3aaea9d64)	CCTBX commit	Tue, 19 Dec 2017 08:39:37 -0700	1130 lines
[git/cctbx] master: mmtbx.prepare_pdb_deposition: More consistent method for separating file extension (99f47a88f)	CCTBX commit	Tue, 19 Dec 2017 12:29:40 +0100	101 lines
[git/cctbx] master: Putative Levenberg-Marquardt minimzer for sdfac_refine. Not quite right yet. (821150940)	CCTBX commit	Mon, 18 Dec 2017 16:28:25 -0800	342 lines
[git/cctbx] master: For lbfgs sdfac_refine, refine the sd terms directly instead of the square of these terms. (1df04973c)	CCTBX commit	Mon, 18 Dec 2017 16:21:30 -0800	240 lines
[git/cctbx] master: Refactor or sdfac_refine in prep for LevMar implementation (a8ff30259)	CCTBX commit	Mon, 18 Dec 2017 15:47:54 -0800	1279 lines
[git/cctbx] master: Add a couple of missing include directives (a309caf0b)	CCTBX commit	Mon, 18 Dec 2017 15:33:40 +0000	105 lines
Jenkins 5a cctbx Tests build 5610 Fixed	DLS Jenkins	Mon, 18 Dec 2017 15:10:18 +0000	37 lines
[git/cctbx] master: bug fix: assert_is_similar_symmetry not always passed along (cbf5a620d)	CCTBX commit	Mon, 18 Dec 2017 15:06:23 +0000	108 lines
Jenkins 5a cctbx Tests build 5609 Unstable	DLS Jenkins	Mon, 18 Dec 2017 04:44:11 +0000	33 lines
[git/cctbx] master: mmtbx.prepare_pdb_deposition: Change default output filename (dd5a96d3d)	CCTBX commit	Sun, 17 Dec 2017 22:47:40 +0100	83 lines
Jenkins 5a cctbx Tests build 5607 Fixed	DLS Jenkins	Sun, 17 Dec 2017 19:10:06 +0000	37 lines
[git/cctbx] master: Fix typo (8722de0fe)	CCTBX commit	Sun, 17 Dec 2017 11:04:52 -0800	81 lines
[git/cctbx] master: wait to check in use_sg_symmetry (426f804db)	CCTBX commit	Sun, 17 Dec 2017 09:41:52 -0800	93 lines
[git/cctbx] master: Allow out-of-cell points if use_sg_symmetry (071124e7f)	CCTBX commit	Sun, 17 Dec 2017 09:33:37 -0800	114 lines
Jenkins 5a cctbx Tests build 5604 Fixed	DLS Jenkins	Sun, 17 Dec 2017 05:21:05 +0000	38 lines
[git/cctbx] master: Fix typo (e4e9197f8)	CCTBX commit	Sun, 17 Dec 2017 05:13:45 +0000	70 lines
[git/cctbx] master: clean clutter (ad835d57e)	CCTBX commit	Sun, 17 Dec 2017 05:13:06 +0000	70 lines
Jenkins 5a cctbx Tests build 5603 Still Failing	DLS Jenkins	Sun, 17 Dec 2017 05:03:46 +0000	160 lines
Jenkins 5a cctbx Tests build 5602 Failure	DLS Jenkins	Sun, 17 Dec 2017 04:58:26 +0000	158 lines
[git/cctbx] master: mmtbx.prepare_pdb_deposition: initial rewrite with new program template (3ffda3b08)	CCTBX commit	Sun, 17 Dec 2017 04:57:04 +0000	546 lines
[git/cctbx] master: Program template: Initial code; more work will follow (b5df2f9fd)	CCTBX commit	Sun, 17 Dec 2017 04:56:11 +0000	830 lines
[git/cctbx] master: fix case where sequences are empty (4e51adc69)	CCTBX commit	Sat, 16 Dec 2017 17:56:24 -0800	77 lines
[git/cctbx] master: clean clutter (56bb013d3)	CCTBX commit	Sat, 16 Dec 2017 13:43:10 -0800	48 lines
[git/cctbx] master: Make get_ncs_from_map similar with and without point-group symmetry (562e0b8e3)	CCTBX commit	Sat, 16 Dec 2017 13:42:52 -0800	531 lines
[git/cctbx] master: clean clutter and set default of false for requiring point group or helical symmetry (2869b52e4)	CCTBX commit	Sat, 16 Dec 2017 10:42:46 -0800	274 lines
[git/cctbx] master: Fix typo in printout (32318462a)	CCTBX commit	Sat, 16 Dec 2017 09:23:14 -0800	79 lines
[git/cctbx] master: use default distance cutoff in split_model; remove excess printout (a44afbf96)	CCTBX commit	Sat, 16 Dec 2017 08:48:16 -0800	430 lines
[git/cctbx] master: Changing RuntimeError to Sorry just in case user would trigger that. Clearer error msg as well. (d775f1c77)	CCTBX commit	Fri, 15 Dec 2017 17:01:32 -0800	116 lines
[git/cctbx] master: Informative message if conflicting restraints. Fix bug with weird input geometry for alt confs. With test. (01060c499)	CCTBX commit	Fri, 15 Dec 2017 15:43:14 -0800	477 lines
[git/cctbx] master: Tidy up output and remove most of the finite differences computation (84cf272e7)	CCTBX commit	Fri, 15 Dec 2017 15:19:39 -0800	384 lines
[git/cctbx] master: Bugfix for sdfac_refine lbfgs (8c863b40b)	CCTBX commit	Fri, 15 Dec 2017 15:17:58 -0800	140 lines
[git/cctbx] master: Refactor to remove some code duplication (0357a9075)	CCTBX commit	Fri, 15 Dec 2017 14:10:59 -0800	400 lines
[git/cctbx] master: clean clutters (deb253e39)	CCTBX commit	Fri, 15 Dec 2017 13:42:45 -0800	48 lines
[git/cctbx] master: Fix import (cff7131a8)	CCTBX commit	Fri, 15 Dec 2017 13:23:11 -0800	133 lines
[git/cctbx] master: Allow another setting of I symmetry (f96c7110c)	CCTBX commit	Fri, 15 Dec 2017 13:17:27 -0800	1097 lines
[git/cctbx] master: Clean clutter (2023fc778)	CCTBX commit	Fri, 15 Dec 2017 13:15:01 -0800	67 lines
[git/cctbx] master: Add lbfgs minimzer for sdfac_refine (9635b9b5f)	CCTBX commit	Fri, 15 Dec 2017 13:00:58 -0800	985 lines
[git/cctbx] master: Bugfixes in cpp code of sdfac_refine (31607de41)	CCTBX commit	Fri, 15 Dec 2017 13:00:57 -0800	207 lines
[git/cctbx] master: Missing part of earlier commit for zeros in normal probabilty plot (5e51a98e6)	CCTBX commit	Fri, 15 Dec 2017 13:00:57 -0800	79 lines
[git/cctbx] master: Add jiffy function for to compute statistics needed downstream and clean up some code duplication (0525af6d1)	CCTBX commit	Fri, 15 Dec 2017 13:00:57 -0800	319 lines
[git/cctbx] master: Change initial values for sdfac_refine (c86a1d3a3)	CCTBX commit	Fri, 15 Dec 2017 13:00:56 -0800	230 lines
[git/cctbx] master: Rename sdfac_refine.target_function to sdfac_refine.sigma_formulation (42d6fa7ad)	CCTBX commit	Fri, 15 Dec 2017 13:00:56 -0800	176 lines
[git/cctbx] master: Clashscore: Change default for keep_hydrogens to False so that it is consistent with MolProbity (35b175d29)	CCTBX commit	Fri, 15 Dec 2017 12:34:44 -0800	102 lines
[git/cctbx] master: Fast and dirty fix. The entire functionality needs massive rewrite/refactoring. (c5e2dfab5)	CCTBX commit	Fri, 15 Dec 2017 12:30:00 -0800	96 lines
[git/cctbx] master: Update min_ncs_cc to set default at 0.75 (73db72f8c)	CCTBX commit	Fri, 15 Dec 2017 11:48:24 -0800	124 lines
[git/cctbx] master: Polygon GUI: added value for Wilson B; change default statistic value to 0 from None to prevent crashing (a0a18bd12)	CCTBX commit	Fri, 15 Dec 2017 11:05:20 -0800	155 lines
[git/cctbx] master: clean_clutter (304706128)	CCTBX commit	Fri, 15 Dec 2017 05:05:55 -0800	48 lines
[git/cctbx] master: Add remove_residue_groups_with_atoms_on_special_positions_selective method; test follows (6cbdf2c1f)	CCTBX commit	Fri, 15 Dec 2017 12:52:35 +0800	157 lines
[git/cctbx] master: Minor printout change; allow similarity in chain_comparison (44530ec00)	CCTBX commit	Thu, 14 Dec 2017 20:14:25 -0700	1047 lines
[git/cctbx] master: clean clutter (a0a55ad63)	CCTBX commit	Fri, 15 Dec 2017 11:03:28 +0800	48 lines
[git/cctbx] master: shift_to_origin method added to pdb.hierarchy (with a test) (9d5f8fa85)	CCTBX commit	Fri, 15 Dec 2017 10:46:58 +0800	180 lines
[git/cctbx] master: Find atom indices in the main copy that bump with the main copy via symmetry or periodicity. There may be several symmetry/periodicity related copies corresponding to given atom in main copy. The function returns a dictionary with keys being atom indices in main copy and values being the list of symmetry operations to generate interacting mates. (aca252ae6)	CCTBX commit	Fri, 15 Dec 2017 10:46:58 +0800	142 lines
[git/cctbx] master: Find atom indices in the main copy that bump with the main copy via symmetry or periodicity. There may be several symmetry/periodicity related copies corresponding to given atom in main copy. The function returns a dictionary with keys being atom indices in main copy and values being the list of symmetry operations to generate interacting mates. (141a1bf9a)	CCTBX commit	Fri, 15 Dec 2017 10:46:58 +0800	106 lines
[git/cctbx] master: Better atom selection cache in model - makes it possible to use 'within' in simple selections (d6a798da8)	CCTBX commit	Thu, 14 Dec 2017 16:58:12 -0800	122 lines
[git/cctbx] master: Fixes for trusted_range in the presence of IMAGE_PEDESTAL (785b564bd)	CCTBX commit	Thu, 14 Dec 2017 15:35:37 +0000	135 lines
[git/cctbx] master: clean clutter (b990b3b6f)	CCTBX commit	Thu, 14 Dec 2017 06:29:02 -0800	48 lines
[git/cctbx] master: Remove minor duplicate effort (4b73528da)	CCTBX commit	Wed, 13 Dec 2017 20:27:02 -0800	82 lines
[git/cctbx] master: Fix typo...forgot to shift ncs position (35a63895d)	CCTBX commit	Wed, 13 Dec 2017 20:07:00 -0800	167 lines
[git/cctbx] master: Allow check_ncs in segment_and_split (d872ebf6a)	CCTBX commit	Wed, 13 Dec 2017 19:32:23 -0800	448 lines
[git/cctbx] master: Teaching pdbtools to understand within keyword in selections. (be72b52ae)	CCTBX commit	Wed, 13 Dec 2017 17:24:14 -0800	302 lines
[git/cctbx] master: modernize example, use new mmCIF dictionary. The validation is not perfect, but validation for freshly downloaded 1yjp.cif is also not perfect... (3328934bb)	CCTBX commit	Wed, 13 Dec 2017 11:38:55 -0800	387 lines
[git/cctbx] master: Adding modern mmCIF model dictionary. It is not used anywhere, but I think it makes sense to have it along with ancient ones. We may actually consider deleting ancient dictionaries. (cd7d91669)	CCTBX commit	Wed, 13 Dec 2017 11:38:55 -0800	65 lines
[git/cctbx] master: Did clean clutter (71e645767)	CCTBX commit	Wed, 13 Dec 2017 09:03:16 +0000	67 lines
[git/cctbx] master: Bugfix for squared formulation of sdfac refine (b38a7070b)	CCTBX commit	Tue, 12 Dec 2017 16:55:13 -0800	85 lines
[git/cctbx] master: MolProbity: Remove redundant paramater for neutron distances (b606cfdfb)	CCTBX commit	Tue, 12 Dec 2017 15:44:30 -0800	186 lines
[git/cctbx] master: Bugfixes for reflection table version of sdfac_refine (33a90605b)	CCTBX commit	Tue, 12 Dec 2017 15:16:13 -0800	227 lines
[git/cctbx] master: Minor printout change (bf73f646c)	CCTBX commit	Tue, 12 Dec 2017 14:01:09 -0700	80 lines
[git/cctbx] master: Allow trimming of helical density to +/- 1 or 2 turns (062ae60fd)	CCTBX commit	Tue, 12 Dec 2017 13:59:35 -0700	425 lines
[git/cctbx] master: Check for presence of file (9519ff26c)	CCTBX commit	Tue, 12 Dec 2017 13:59:35 -0700	79 lines
[git/cctbx] master: clang bug fix: Avoid dereferencing of NULL pointers (95759230c)	CCTBX commit	Tue, 12 Dec 2017 12:54:23 -0800	107 lines
[git/cctbx] master: Added more output when testing FormatNexus (ebb84df73)	CCTBX commit	Tue, 12 Dec 2017 16:54:52 +0000	108 lines
[git/cctbx] master: Do not attempt to build wxPython for Python3 (d63df0f67)	CCTBX commit	Tue, 12 Dec 2017 12:50:33 +0000	80 lines
[git/cctbx] master: Forgot a space (4844b38eb)	CCTBX commit	Mon, 11 Dec 2017 17:04:01 -0800	82 lines
[git/cctbx] master: MolProbity/clashscore bug fix: Pass hydrogen and nuclear options to clashscore calculation in MolProbity for consistent results (3fb2bc87b)	CCTBX commit	Mon, 11 Dec 2017 16:49:06 -0800	230 lines
[git/cctbx] master: Revert unintended portion of last commit (49de575a4)	CCTBX commit	Mon, 11 Dec 2017 16:25:24 -0800	112 lines
[git/cctbx] master: Alternate formulation of sdfac equation using squared parameters (f8ab792e6)	CCTBX commit	Mon, 11 Dec 2017 16:09:25 -0800	411 lines
[git/cctbx] master: Better OpenMP block for nanoBragg. (d9592c2fd)	CCTBX commit	Mon, 11 Dec 2017 15:42:30 -0800	144 lines
[git/cctbx] master: Also move minimizer for refl table version (643539514)	CCTBX commit	Mon, 11 Dec 2017 15:33:34 -0800	472 lines
[git/cctbx] master: Bugfix for sdfac_refine. Get counters in sync. (1c096d1e1)	CCTBX commit	Mon, 11 Dec 2017 15:33:34 -0800	94 lines
[git/cctbx] master: sdfac_refine: move simplex minimzer object out of function definition (e8ff2c03f)	CCTBX commit	Mon, 11 Dec 2017 15:33:33 -0800	428 lines
[git/cctbx] master: missed variable renames (166f1521f)	CCTBX commit	Mon, 11 Dec 2017 23:20:18 +0000	86 lines
[git/cctbx] master: clean clutter (c3ffe8afc)	CCTBX commit	Mon, 11 Dec 2017 16:11:50 -0700	48 lines
[git/cctbx] master: fix bug in bioinformatics where line with just > was not ignored (72692011c)	CCTBX commit	Mon, 11 Dec 2017 16:10:18 -0700	92 lines
[git/cctbx] master: validation GUI table for ratamers now displays blanks instead of None for unassessible chi angles (c9d8aed46)	CCTBX commit	Mon, 11 Dec 2017 14:58:58 -0500	101 lines
[git/cctbx] master: added stoplight cutoffs for Rama Favored for the GUI validation summary page (1f9d86d36)	CCTBX commit	Mon, 11 Dec 2017 14:57:19 -0500	85 lines
[git/cctbx] master: Add dev.cxi.mpi_merge_refltable (da37e0d55)	CCTBX commit	Mon, 11 Dec 2017 10:45:49 -0800	445 lines
[git/cctbx] master: Nicer error message with images missing from sweeps (2bb437800)	CCTBX commit	Mon, 11 Dec 2017 16:37:17 +0000	118 lines
[git/cctbx] master: double duh (6d2835d12)	CCTBX commit	Mon, 11 Dec 2017 01:18:43 -0800	68 lines
[git/cctbx] master: Temporarily avoid prebuilt numpy package, see #95 for details (eb6439d7a)	CCTBX commit	Mon, 11 Dec 2017 09:12:50 +0000	238 lines
[git/cctbx] master: duh (22a22ced6)	CCTBX commit	Mon, 11 Dec 2017 00:41:31 -0800	277 lines
[git/cctbx] master: need correct path (be2dfe1e7)	CCTBX commit	Sun, 10 Dec 2017 23:55:34 -0800	84 lines
[git/cctbx] master: Remove inline classes inside OpenMP pragma structure, Centos 6 cannot parse. (cfbcd38d1)	CCTBX commit	Sun, 10 Dec 2017 21:22:40 -0800	917 lines
[git/cctbx] master: test for getting the same output from clashscore and molprobity (0a94df945)	CCTBX commit	Sun, 10 Dec 2017 19:11:51 -0800	71 lines
[git/cctbx] master: clean_clutter (861274833)	CCTBX commit	Sun, 10 Dec 2017 16:32:52 -0800	48 lines
[git/cctbx] master: Set chain type for individual fragments (18a01f654)	CCTBX commit	Sun, 10 Dec 2017 09:46:45 -0800	104 lines
[git/cctbx] master: exclude CE1 from metal linking and CD2 (7b6e68cd8)	CCTBX commit	Sat, 9 Dec 2017 20:27:50 -0800	81 lines
[git/cctbx] master: exclude CE1 from metal linking (a0bc25c08)	CCTBX commit	Sat, 9 Dec 2017 20:25:15 -0800	164 lines
[git/cctbx] master: test fix (f487781ba)	CCTBX commit	Sat, 9 Dec 2017 18:45:09 -0800	104 lines
[git/cctbx] master: remove useless output (11b20bdb9)	CCTBX commit	Sat, 9 Dec 2017 18:03:06 -0800	72 lines
[git/cctbx] master: Allow automatic splitting of chains in split_model (e5dfe9876)	CCTBX commit	Sat, 9 Dec 2017 13:40:31 -0800	247 lines
[git/cctbx] master: fix print formatting (c2347d094)	CCTBX commit	Sat, 9 Dec 2017 18:25:52 +0000	109 lines
[git/cctbx] master: OK proper fix for xia2/xia2#200 make sure that the mosflm beam always points at the detector (c9c2d56ed)	CCTBX commit	Sat, 9 Dec 2017 15:56:54 +0000	115 lines
[git/cctbx] master: Validation: add more Polygon statistics (510a05780)	CCTBX commit	Fri, 8 Dec 2017 17:00:31 -0800	268 lines
[git/cctbx] master: OpenMP parallelizes around the outer loop. Results invariant to OMP_NUM_THREADS. Optimal is 8 threads only. (bc9406807)	CCTBX commit	Fri, 8 Dec 2017 16:46:21 -0800	371 lines
[git/cctbx] master: OpenMP pragma works at inner loop level but there is no speedup. (8634c7948)	CCTBX commit	Fri, 8 Dec 2017 16:46:21 -0800	544 lines
[git/cctbx] master: Partial progress. Mosaicity tic now const correct. (0efde3e78)	CCTBX commit	Fri, 8 Dec 2017 16:46:20 -0800	711 lines
[git/cctbx] master: Get rid of compile warnings. (28b7e5987)	CCTBX commit	Fri, 8 Dec 2017 16:46:20 -0800	84 lines
[git/cctbx] master: Work in progress. Develop an alternate add_nanoBragg_spots() to support OpenMP. (09f99a1c1)	CCTBX commit	Fri, 8 Dec 2017 16:46:20 -0800	1135 lines
[git/cctbx] master: Rename cpp file (095c6e2d7)	CCTBX commit	Fri, 8 Dec 2017 16:08:15 -0800	650 lines
[git/cctbx] master: Implementation of errors_from_sample_residuals using reflection tables (4643e1d12)	CCTBX commit	Fri, 8 Dec 2017 16:08:15 -0800	238 lines
[git/cctbx] master: Implementation of sdfac_refine using reflection tables. (4d13bd6c8)	CCTBX commit	Fri, 8 Dec 2017 16:08:14 -0800	918 lines
[git/cctbx] master: Adapt tests. (22605a8a8)	CCTBX commit	Fri, 8 Dec 2017 14:02:57 -0800	504 lines
[git/cctbx] master: Adapt reset of self.x when there is xyz selection. (2c95feffd)	CCTBX commit	Fri, 8 Dec 2017 10:29:46 -0800	133 lines
[git/cctbx] master: Make selection of riding manager available in model. (73d81608a)	CCTBX commit	Fri, 8 Dec 2017 10:27:22 -0800	139 lines
[git/cctbx] master: Clean clutter (1bfa97dfe)	CCTBX commit	Thu, 7 Dec 2017 16:15:29 -0700	48 lines
[git/cctbx] master: chain_comparison allow selection of close/far parts (1f6d50ca5)	CCTBX commit	Thu, 7 Dec 2017 14:07:11 -0800	652 lines
[git/cctbx] master: More bug fixes for dev.cxi.merge_refltable (4629681e2)	CCTBX commit	Thu, 7 Dec 2017 10:32:56 -0800	114 lines
[git/cctbx] master: Bugfix for dev.cxi.merge_refltable when not using postrefinement (6a113573f)	CCTBX commit	Thu, 7 Dec 2017 09:10:32 -0800	94 lines
[git/cctbx] master: Bugfixes for dev.cxi.merge_refltable (0514baed7)	CCTBX commit	Thu, 7 Dec 2017 08:50:26 -0800	115 lines
[git/cctbx] master: Disable PyRTF for Python3 builds. See #108 (3892950b1)	CCTBX commit	Thu, 7 Dec 2017 15:00:36 +0000	80 lines
[git/cctbx] master: Mask=>Bool; fixes #107 (2f8c03b1a)	CCTBX commit	Thu, 7 Dec 2017 09:55:30 +0000	81 lines
[git/cctbx] master: Bugfix for cxi.merge postrefinment rs_hybrid (81c8c5e8d)	CCTBX commit	Wed, 6 Dec 2017 16:18:25 -0800	82 lines
[git/cctbx] master: More sdfac_refine improvements (d743f38ee)	CCTBX commit	Wed, 6 Dec 2017 16:14:17 -0800	323 lines
[git/cctbx] master: For sdfac_refine, better handle sigma < 0 in compute_normalized_deviations (32f51768b)	CCTBX commit	Wed, 6 Dec 2017 16:14:17 -0800	156 lines
[git/cctbx] master: MI: fix: geometry minimization wasn't updating coordinates. (0f2cf3244)	CCTBX commit	Wed, 6 Dec 2017 15:57:37 -0800	85 lines
[git/cctbx] master: added error output (852feecd9)	CCTBX commit	Wed, 6 Dec 2017 15:32:36 -0800	76 lines
[git/cctbx] master: Rearrange. Avoid -if x in list- for speed gain. (c9f877a78)	CCTBX commit	Wed, 6 Dec 2017 15:24:11 -0800	351 lines
[git/cctbx] master: Refactor error modeling in cxi.merge by moving sdfac_refine and errors_from_sample_residuals into separate class files (24bf9cd02)	CCTBX commit	Wed, 6 Dec 2017 15:20:28 -0800	1678 lines
[git/cctbx] master: macOS installer: Fixes bug where SSL_CERT_FILE is not correct when creating the graphical installer for macOS (c2b86defb)	CCTBX commit	Wed, 6 Dec 2017 14:55:40 -0800	119 lines
[git/cctbx] master: output reasonable precision in mmCIF (70d3a4def)	CCTBX commit	Wed, 6 Dec 2017 13:18:51 -0800	417 lines
[git/cctbx] master: Make deep_copy more compact. (1f06c8c35)	CCTBX commit	Wed, 6 Dec 2017 11:43:50 -0800	391 lines
[git/cctbx] master: clean clutter (4ffbb7186)	CCTBX commit	Wed, 6 Dec 2017 10:21:14 -0800	48 lines
[git/cctbx] master: Updated help string in cell_rejection (cd28f1cd3)	CCTBX commit	Wed, 6 Dec 2017 09:54:43 -0800	89 lines
[git/cctbx] master: Updated cxi_merge.py for cell rejection (79c1d9424)	CCTBX commit	Wed, 6 Dec 2017 09:54:43 -0800	126 lines
[git/cctbx] master: Update function for riding H manager. (dc04ffe9a)	CCTBX commit	Wed, 6 Dec 2017 09:53:20 -0800	105 lines
[git/cctbx] master: Alternate interface for setting the A-matrix, critical for XFEL simulations (3514d25cc)	CCTBX commit	Tue, 5 Dec 2017 20:36:03 -0800	250 lines
[git/cctbx] master: cleanup (8cc521def)	CCTBX commit	Tue, 5 Dec 2017 17:05:08 -0800	1158 lines
[git/cctbx] master: Use old idealize_h for now until water can be parameterized. (8fdcfd773)	CCTBX commit	Tue, 5 Dec 2017 16:57:42 -0800	491 lines
[git/cctbx] master: new test (37035e307)	CCTBX commit	Tue, 5 Dec 2017 16:33:27 -0800	439 lines
[git/cctbx] master: Cleanup. (ccad98753)	CCTBX commit	Tue, 5 Dec 2017 15:13:56 -0800	243 lines
[git/cctbx] master: changes to validation gui column widths for readability (441371b73)	CCTBX commit	Tue, 5 Dec 2017 16:55:18 -0500	206 lines
[git/cctbx] master: safeguarding (a062f37e0)	CCTBX commit	Tue, 5 Dec 2017 12:02:46 -0800	76 lines
[git/cctbx] master: Added function to experiment list to nullify single file reader (9e2b4e35a)	CCTBX commit	Tue, 5 Dec 2017 13:31:03 +0000	90 lines
[git/cctbx] master: Expanding MTRIX by default in model. Leads to phenix_regression/model_vs_data/run_tests.py failing due to bad matrices.... How come it was ok before? (2401ccd98)	CCTBX commit	Mon, 4 Dec 2017 19:09:55 -0800	903 lines
[git/cctbx] master: Select method for riding H manager. With test. (15dd588f6)	CCTBX commit	Mon, 4 Dec 2017 15:03:13 -0800	697 lines
[git/cctbx] master: Increase parameters saved by cxi.merge and dev.cxi.merge_refltable (a8e9bb9f4)	CCTBX commit	Mon, 4 Dec 2017 12:48:41 -0800	315 lines
[git/cctbx] master: Add test for deep_copy in riding H manager. (a54d14e5a)	CCTBX commit	Sun, 3 Dec 2017 22:38:47 -0800	418 lines
[git/cctbx] master: Deep_copy for riding_H manager. (24be3d71c)	CCTBX commit	Sun, 3 Dec 2017 21:00:31 -0800	184 lines
[git/cctbx] master: Slight re-arrangement. (1ab33b130)	CCTBX commit	Sun, 3 Dec 2017 17:46:18 -0800	171 lines
[git/cctbx] master: Cleanup. (1aa16fadc)	CCTBX commit	Sun, 3 Dec 2017 17:27:40 -0800	217 lines
[git/cctbx] master: Tests for getter, setter and copy in riding_coefficients. (b40951c9c)	CCTBX commit	Sun, 3 Dec 2017 15:06:46 -0800	340 lines
[git/cctbx] master: Make setter for riding_coefficients. (c98e8b222)	CCTBX commit	Sun, 3 Dec 2017 14:26:08 -0800	222 lines
[git/cctbx] master: clean clutter (b2cad72a0)	CCTBX commit	Sun, 3 Dec 2017 06:38:15 -0800	48 lines
[git/cctbx] master: Ignore refinement errors in absolute scaling in auto_sharpen; fix minor bugs in chain_comparison (030449909)	CCTBX commit	Sun, 3 Dec 2017 06:21:22 -0800	236 lines
[git/cctbx] master: remove unused imports (9cc20f6ab)	CCTBX commit	Sat, 2 Dec 2017 16:57:45 -0800	73 lines
[git/cctbx] master: remove unused imports (2bf1a1e0c)	CCTBX commit	Sat, 2 Dec 2017 16:49:08 -0800	73 lines
[git/cctbx] master: Download OpenSSL from dependencies repository. Partially reverts commit 3f979fff16d0e15a664457ee506452a828e9d187. (3a1b0e860)	CCTBX commit	Sun, 3 Dec 2017 00:44:41 +0000	116 lines
[git/cctbx] master: This test now brakes due to riding model not fucntioning correctly in this case. For Dorothee to fix. (c5fd2d02f)	CCTBX commit	Sat, 2 Dec 2017 16:33:56 -0800	125 lines
[git/cctbx] master: Test to exercise metal coordination links. Currently fails. For Nigel to fix. (6ba1c0e3a)	CCTBX commit	Sat, 2 Dec 2017 16:33:56 -0800	636 lines
[git/cctbx] master: This does not Reduce anymore. (e690e3e05)	CCTBX commit	Sat, 2 Dec 2017 16:33:56 -0800	147 lines
[git/cctbx] master: Remove Reduce-based .idealize_h(): there is no point to have it given we have Dorothee's riding model! This will brake something. (f68801dcf)	CCTBX commit	Sat, 2 Dec 2017 16:33:56 -0800	369 lines
[git/cctbx] master: fix clutter (75b31c0cf)	CCTBX commit	Sat, 2 Dec 2017 05:19:17 -0800	48 lines
[git/cctbx] master: Set region_weight_default=30 (was 40 or resolution_dependent); allow iteration_fraction as parameter (335461490)	CCTBX commit	Fri, 1 Dec 2017 20:32:51 -0800	322 lines
[git/cctbx] master: ss_idealization is now aware of cartesian NCS. With test. (8d4858850)	CCTBX commit	Fri, 1 Dec 2017 18:16:25 -0800	1647 lines
[git/cctbx] master: OpenSSL: Update to 1.0.2m Change download URL to openssl.org (3f979fff1)	CCTBX commit	Fri, 1 Dec 2017 16:52:56 -0800	115 lines
[git/cctbx] master: Some cleanup (22a041c9d)	CCTBX commit	Fri, 1 Dec 2017 12:17:17 -0800	914 lines
[git/cctbx] master: Fix for rare occasions where chains have different ions and they are mixed in alignment procedure. Therefore additional filter is added. In such cases some legitimate ion mathes could be missed. (89471e512)	CCTBX commit	Fri, 1 Dec 2017 12:01:03 -0800	113 lines
[git/cctbx] master: Deprecate experimental programs for merging (30f4287c9)	CCTBX commit	Fri, 1 Dec 2017 11:57:16 -0800	214 lines
[git/cctbx] master: Remove the dependency of mpi merge on single node merge (0a5703246)	CCTBX commit	Fri, 1 Dec 2017 11:50:48 -0800	147 lines
[git/cctbx] master: Some refactoring. (320d1fcd1)	CCTBX commit	Fri, 1 Dec 2017 10:42:17 -0800	237 lines
[git/cctbx] master: Revert "Rescope show_overall_observations as a static method in cxi_merge.scaling_manager" (4510d9435)	CCTBX commit	Fri, 1 Dec 2017 10:15:32 -0800	1257 lines
[git/cctbx] master: Changes for saving per-frame information in a separate table during merging (b48abb980)	CCTBX commit	Fri, 1 Dec 2017 09:14:50 -0800	346 lines
[git/cctbx] master: Remove old comment, and make single_reflection_histograms a static method (7ba7f822d)	CCTBX commit	Fri, 1 Dec 2017 08:56:58 -0800	399 lines
[git/cctbx] master: Rescope show_overall_observations as a static method in cxi_merge.scaling_manager (e1dec1822)	CCTBX commit	Fri, 1 Dec 2017 08:56:58 -0800	1251 lines
[git/cctbx] master: Add development version of cxi.merge that uses a reflection table (86723b7f7)	CCTBX commit	Fri, 1 Dec 2017 08:56:58 -0800	899 lines
[git/cctbx] master: found this investigating an issue (e1a4b73ba)	CCTBX commit	Fri, 1 Dec 2017 11:50:28 +0000	76 lines
[git/cctbx] master: Should be a fix for pickling bug (6beefb136)	CCTBX commit	Thu, 30 Nov 2017 16:37:27 -0800	175 lines
[git/cctbx] master: Make the base class compatible with the derived class using MPI. (391b08b93)	CCTBX commit	Thu, 30 Nov 2017 15:57:19 -0800	216 lines
[git/cctbx] master: Refactored the MPI version to inherit from the base Script. (12a83571e)	CCTBX commit	Thu, 30 Nov 2017 15:57:18 -0800	496 lines

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