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Subject	From	Date	Size
[git/cctbx] master: Print out when we are using the psana HDF5 include path when building cbflib_adaptbx (c8a988f07)	CCTBX Commit via DLS Jenkins	Fri, 31 Mar 2017 14:15:36 -0700	79 lines
[git/cctbx] master: ignore me (7bb52d070)	CCTBX Commit via DLS Jenkins	Fri, 31 Mar 2017 12:19:17 -0700	63 lines
[git/cctbx] master: minor changes to CBF writer and special SMV input (d0b8fec6e)	CCTBX Commit via DLS Jenkins	Fri, 31 Mar 2017 12:19:17 -0700	186 lines
[git/cctbx] master: had to add image_pedestal, but "raw_data -= image_pedestal" is still a horrible idea files already affected are FormatSMVADSCS*.py and FormatSMVRigakuSaturnNoTS.py (21e9de007)	CCTBX Commit via DLS Jenkins	Fri, 31 Mar 2017 12:19:17 -0700	219 lines
[git/cctbx] master: moving simtbx into cctbx (079335016)	CCTBX Commit via DLS Jenkins	Fri, 31 Mar 2017 12:19:17 -0700	88 lines
Jenkins 5b cctbx MacOS build 1068 Fixed	Jenkins Build Server (Diamond)	Fri, 31 Mar 2017 18:35:22 +0100	37 lines
[git/cctbx] master: Rayoinx CBF from XTC: handle the beam center override. (5144669ed)	CCTBX Commit via DLS Jenkins	Fri, 31 Mar 2017 09:59:07 -0700	119 lines
Jenkins 5b cctbx MacOS build 1067 Unstable	Jenkins Build Server (Diamond)	Fri, 31 Mar 2017 17:14:01 +0100	34 lines
[git/cctbx] master: Bugfix for rayonix cbfs. (839a5f3dc)	CCTBX Commit via DLS Jenkins	Fri, 31 Mar 2017 09:00:50 -0700	231 lines
[git/cctbx] master: Add parameter format.cbf.mode = *cspad rayonix to cctbx.xfel.xtc_dump to enable dumping rayonix cbfs. (572558763)	CCTBX Commit via DLS Jenkins	Thu, 30 Mar 2017 21:59:08 -0700	340 lines
[git/cctbx] master: Toolbox code for reading data from a rayonix detector from and XTC stream and creating a full imagecif representation of it. (707ab688d)	CCTBX Commit via DLS Jenkins	Thu, 30 Mar 2017 21:59:08 -0700	931 lines
[git/cctbx] master: Add FormatCBFFullStill as an additional class in FormatCBFFull. (a171a5533)	CCTBX Commit via DLS Jenkins	Thu, 30 Mar 2017 21:59:07 -0700	295 lines
[git/cctbx] master: Rejigger FormatCBFCspadInMemory. (2d86bc994)	CCTBX Commit via DLS Jenkins	Thu, 30 Mar 2017 21:59:07 -0700	114 lines
[git/cctbx] master: Bugfix: calculate overall multiplicity w.r.t. # possible. (c72a692b0)	CCTBX Commit via DLS Jenkins	Thu, 30 Mar 2017 09:31:20 -0700	83 lines
[git/cctbx] master: dials.image_viewer: bug fix resulting from over-optimisation of image viewer performance (d1ee021d6)	CCTBX Commit via DLS Jenkins	Thu, 30 Mar 2017 10:59:28 +0100	77 lines
[git/cctbx] master: Removed problematic format class (2b6071f56)	CCTBX Commit via DLS Jenkins	Thu, 30 Mar 2017 09:15:00 +0100	248 lines
[git/cctbx] master: Break phil parameter ambiguity where possible by lower expert level. If ambiguity can be resolved print a warning. It ambiguity can't be resolved, fail. Fixes #8 (7557b74c5)	CCTBX Commit via DLS Jenkins	Thu, 30 Mar 2017 01:11:30 +0100	130 lines
[git/cctbx] master: Create a detectorbase so dials_regression/test.py doesn't choke on this Format (but I don't think it uses detectorbase for anything otherwise) (c87c7b22b)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 22:40:23 +0100	82 lines
[git/cctbx] master: Add option max_delta=None for cctbx.xfel.filter_experiments_by_rmsd. (af1d7da33)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 13:01:10 -0700	114 lines
[git/cctbx] master: Bugfix (check limits for plot) (fb1776fe2)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 13:00:05 -0700	77 lines
[git/cctbx] master: cctbx.xfel.xtc_dump changes. (52080dd90)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 12:40:51 -0700	186 lines
[git/cctbx] master: remove unnecessary text (19460364a)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 12:35:40 -0600	76 lines
[git/cctbx] master: Fixed test and added format class for CBF converted from Tiff (e63b3c137)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 16:32:37 +0100	456 lines
[git/cctbx] master: Added from phil function to detector (d6b78ad64)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 15:38:24 +0100	1580 lines
[git/cctbx] master: Fixed a couple of bits to allow complete specification of metadata from command line parameters (i.e. use a site file in dials.import) (4a5ea3f95)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 15:38:24 +0100	349 lines
[git/cctbx] master: Added scan from_phil function and test (241c8c32a)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 15:38:24 +0100	328 lines
[git/cctbx] master: Set distance better (a9c91b4a2)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 15:38:24 +0100	466 lines
[git/cctbx] master: Added goniometer from phil and did a clean clutter (6571bc7d4)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 15:38:24 +0100	653 lines
[git/cctbx] master: Added from_phil function to beam (0283bcb80)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 15:38:24 +0100	270 lines
[git/cctbx] master: bug fix (f8a79ca2f)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 14:19:18 +0100	80 lines
[git/cctbx] master: method to read a Bruker text header into a list of 80 char lines (738ead8c9)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 13:48:38 +0100	158 lines
[git/cctbx] master: not required (4be1f3bc6)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 13:48:38 +0100	73 lines
[git/cctbx] master: Format for Bruker PHOTON-II CPAD (ad91509d6)	CCTBX Commit via DLS Jenkins	Wed, 29 Mar 2017 13:48:38 +0100	448 lines
[git/cctbx] master: Exposing parameter to hide labels on Ramachandran plots to the CL tool (662c80aef)	CCTBX Commit via DLS Jenkins	Tue, 28 Mar 2017 16:57:46 -0700	168 lines
[git/cctbx] master: Notice for further generations. (ffed46b65)	CCTBX Commit via DLS Jenkins	Tue, 28 Mar 2017 09:44:19 -0700	85 lines
[git/cctbx] master: Seems to be a fix to a bug reported by user. Procedure failed deeper inside, in the second macro-cycle of phenix.refine. So keeping the old manager could be a problem and this change seems to be fixing the bug. (67af93785)	CCTBX Commit via DLS Jenkins	Mon, 27 Mar 2017 14:02:27 -0700	141 lines
[git/cctbx] master: Spelling (4c2f53be5)	CCTBX Commit via DLS Jenkins	Mon, 27 Mar 2017 12:54:31 -0700	112 lines
[git/cctbx] master: Add parameter round_and_orthagonalize=True to cxi.calibdir2cbfheader (a39e159c4)	CCTBX Commit via DLS Jenkins	Mon, 27 Mar 2017 12:43:09 -0700	268 lines
[git/cctbx] master: dxtbx.plot_detector_models: bugfix and handle datablocks (338235f6e)	CCTBX Commit via DLS Jenkins	Mon, 27 Mar 2017 08:44:12 -0700	135 lines
[git/cctbx] master: Always applu trusted range mask (d6ee93cd2)	CCTBX Commit via DLS Jenkins	Mon, 27 Mar 2017 13:06:49 +0100	157 lines
[git/cctbx] master: Try to fix eiger nexus reading: - invert beam direction - invert detector origin - invert detector fast axis - invert detector slow axis (ede9683a5)	CCTBX Commit via DLS Jenkins	Mon, 27 Mar 2017 10:29:59 +0100	104 lines
[git/cctbx] master: Added test for VAL (e236d84d3)	CCTBX Commit via DLS Jenkins	Sun, 26 Mar 2017 12:55:04 -0700	354 lines
[git/cctbx] master: Added flipping of VAL, LEU Added test for LEU Typos (bb984693f)	CCTBX Commit via DLS Jenkins	Sun, 26 Mar 2017 12:25:27 -0700	753 lines
[git/cctbx] master: small variable change (0c7e0ed01)	CCTBX Commit via DLS Jenkins	Sun, 26 Mar 2017 09:41:32 -0700	78 lines
[git/cctbx] master: Don't fail if the difference is MSE-MET. (83fe878b0)	CCTBX Commit via DLS Jenkins	Fri, 24 Mar 2017 20:45:34 -0700	106 lines
[git/cctbx] master: Initial legacy work to apply existing quad/tile translations from image pickle style CSPAD metrology to new style CBF headers. (ad307c10a)	CCTBX Commit via DLS Jenkins	Fri, 24 Mar 2017 17:49:51 -0700	291 lines
[git/cctbx] master: fix minor bugs in segment_and_split for cases withouth ncs (aab31202f)	CCTBX Commit via DLS Jenkins	Fri, 24 Mar 2017 14:55:49 -0600	135 lines
[git/cctbx] master: Allow target for choosing unique chains; keep used ncs ops in segment_and_split (c7c072aff)	CCTBX Commit via DLS Jenkins	Fri, 24 Mar 2017 14:31:01 -0600	808 lines
[git/cctbx] master: A bit more informative output. (2a6623f94)	CCTBX Commit via DLS Jenkins	Thu, 23 Mar 2017 11:24:31 -0700	110 lines
[git/cctbx] master: Allow seletion of ncs operators in ncs.py deep_copy (a793d59c4)	CCTBX Commit via DLS Jenkins	Thu, 23 Mar 2017 12:17:14 -0600	370 lines
[git/cctbx] master: Suggested template and design for command-line tools along with simple example of functionality for discussion. (8e1ab5477)	CCTBX Commit via DLS Jenkins	Thu, 23 Mar 2017 10:57:27 -0700	3231 lines
[git/cctbx] master: Loosen test a bit to account for Centos 5 32 bit test platform on buildbot. (f50923608)	CCTBX Commit via DLS Jenkins	Thu, 23 Mar 2017 08:36:00 -0700	95 lines
[git/cctbx] master: Image viewer no longer depends on iotbx/detectors/detectorbase interface, while at the same time active area display is preserved for Pilatus and Eiger detector types. This is supported by introducing a new get_vendortype() method in the dxtbx/format class, intended for use by the flex_image generator. (ab784cceb)	CCTBX Commit via DLS Jenkins	Wed, 22 Mar 2017 14:36:31 -0700	581 lines
[git/cctbx] master: cctbx.crystal.reindex.reindexing_operators: bug fix; solves #18 (42c89670b)	CCTBX Commit via DLS Jenkins	Wed, 22 Mar 2017 11:15:59 +0900	74 lines
[git/cctbx] master: Add option known_orientations_folder. (dcb36697b)	CCTBX Commit via DLS Jenkins	Tue, 21 Mar 2017 16:57:12 -0700	152 lines
[git/cctbx] master: cspad.detector_congruence2: add weighted standard deviation to delta XYZ columns. (b0c7c71be)	CCTBX Commit via DLS Jenkins	Tue, 21 Mar 2017 12:40:32 -0700	304 lines
[git/cctbx] master: dxtbx.detector_superpose fixes (b6ed39212)	CCTBX Commit via DLS Jenkins	Tue, 21 Mar 2017 12:37:03 -0700	228 lines
[git/cctbx] master: Only add neighbors if ncs is present (d3d3c4187)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 19:25:14 -0600	80 lines
[git/cctbx] master: Set criteria for adding neighbors (0c62aba4b)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 19:20:59 -0600	110 lines
[git/cctbx] master: Catch empty chain (eb029a81d)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 18:16:21 -0600	75 lines
[git/cctbx] master: Allow adding in neighbors (5a22809fb)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 17:43:11 -0600	311 lines
[git/cctbx] master: cspad.detector_congruence2: add dR and dT (radial and transverse displacements) to lab deltas table. (fb4d31120)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 14:39:37 -0700	320 lines
[git/cctbx] master: Mods for cspad.detector_congruence2: add dXY and change dX and dY to signed quantities (bf4d1da5a)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 13:48:28 -0700	539 lines
[git/cctbx] master: Add delta X, Y, Z and overall displacements to cspad.detector_congruence2 (0ff45f774)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 13:23:33 -0700	688 lines
[git/cctbx] master: minor bugfixes to LSF queueing (738334499)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 12:32:02 -0700	755 lines
[git/cctbx] master: Bugfix (0fb630c76)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 11:22:22 -0700	236 lines
[git/cctbx] master: Add orthographic projection option to dxtbx.plot_detector_models (471136ebb)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 10:53:09 -0700	260 lines
[git/cctbx] master: In dxtbx.plot_detector_models, annotate plot with panel numbers (20cd7d733)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 10:38:23 -0700	102 lines
[git/cctbx] master: Modify cspad.cbf_metrology to allow split_dataset=True even if data_phil=True (445e095c5)	CCTBX Commit via DLS Jenkins	Mon, 20 Mar 2017 10:36:47 -0700	240 lines
[git/cctbx] master: Patch of bug fixes from Ben Barad for EM Ringer (b587ccbf3)	CCTBX Commit via DLS Jenkins	Sun, 19 Mar 2017 11:02:58 -0700	392 lines
[git/cctbx] master: Fix labels (02772c19a)	CCTBX Commit via DLS Jenkins	Sat, 18 Mar 2017 14:47:45 -0700	87 lines
[git/cctbx] master: Output human readable interpretation for correlation coefficients. (b44631948)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 17:37:07 -0700	198 lines
[git/cctbx] master: Add to the cspad.detector_congruence2 report a table with changes between the detectors, but only relative to the local frames of the panel groups. (7e1755fe1)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 17:13:22 -0700	559 lines
[git/cctbx] master: Add deviations of euler angles of panel groups in lab space to report in cspad.detector_congruence2. (d3ad2d72c)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 17:13:22 -0700	468 lines
[git/cctbx] master: Add first bits to lab coordinates table of cspad.detector_congruence2. (e754680c9)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 17:13:21 -0700	504 lines
[git/cctbx] master: Begin rewrite of cspad.detector_congruence (6cf2c7129)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 17:13:21 -0700	1110 lines
[git/cctbx] master: finally... (cdac92cec)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 16:26:58 -0700	524 lines
[git/cctbx] master: rename a new file (d14e5b2ef)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 14:57:12 -0700	524 lines
[git/cctbx] master: Merge pull request #20 from cctbx/tile_generation_com_origin (b5442476f)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 14:34:28 -0700	56 lines
[git/cctbx] master: need to add the test script here (e57daab69)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 14:30:08 -0700	68 lines
[git/cctbx] master: Added test for improved cis/trans (e8e881adb)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 14:28:30 -0700	88 lines
[git/cctbx] master: here it really is... (697c93292)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 14:28:30 -0700	524 lines
[git/cctbx] master: more flexible and correct omega defs (15fcd04f4)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 14:28:29 -0700	221 lines
[git/cctbx] master: Enable excluding one CSPAD sensor's data (as a test). (f4129a645)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 14:15:45 -0700	262 lines
[git/cctbx] master: Integration pickle (mapped predictions) viewer tool. (a5292cc5a)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 13:59:24 -0700	281 lines
[git/cctbx] master: clean clutter (a8cbd4186)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 13:49:07 -0700	76 lines
[git/cctbx] master: Use center of mass for calculation of tile transformations Partially reverts e6d11ba698a38cdb0fc86e120e7cdf75d2292456. (162a0adf7)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 16:27:42 -0400	215 lines
[git/cctbx] master: Windows compilation fixes for cbflib_adaptbx and for crystal.h after moving from svn to git for cbflib. (f1f312166)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 13:01:38 -0700	74 lines
[git/cctbx] master: Image pickle path and filename utils. (ce706cb9a)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 12:51:46 -0700	249 lines
[git/cctbx] master: Predictions multiplicity in merging. (c6b81ac29)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 12:49:02 -0700	439 lines
[git/cctbx] master: Prediction multiplicity calculation in merging. (939794bf4)	CCTBX Commit via DLS Jenkins	Fri, 17 Mar 2017 12:37:23 -0700	935 lines
[git/cctbx] master: skip k_sol for auto_sharpen as it my miscalculate FC (60a9147fc)	CCTBX Commit via DLS Jenkins	Thu, 16 Mar 2017 20:28:08 -0600	168 lines
[git/cctbx] master: saving tried rama outside loop idealization for rsr (3e24e571b)	CCTBX Commit via DLS Jenkins	Thu, 16 Mar 2017 14:31:54 -0700	242 lines
[git/cctbx] master: Making flip_symmetric_amino_acids parameter accessible via search in GUI (877c83351)	CCTBX Commit via DLS Jenkins	Thu, 16 Mar 2017 14:22:04 -0700	79 lines
[git/cctbx] master: Make multiresidue class consistent with ramalyze in terms of cis-peptide validation (1448e2999)	CCTBX Commit via DLS Jenkins	Thu, 16 Mar 2017 14:22:04 -0700	79 lines
[git/cctbx] master: Add overall displacements to cspad.detector_congruence (0205729af)	CCTBX Commit via DLS Jenkins	Thu, 16 Mar 2017 13:24:55 -0700	298 lines
[git/cctbx] master: Add overall offset sigma column to report from cspad.detector_congruence. (54154f4be)	CCTBX Commit via DLS Jenkins	Thu, 16 Mar 2017 12:00:05 -0700	282 lines
[git/cctbx] master: dxtbx.detector_superpose: utility to superpose a moving detector onto a reference detector. (aee1ef03d)	CCTBX Commit via DLS Jenkins	Thu, 16 Mar 2017 10:31:25 -0700	356 lines
[git/cctbx] master: this rotation axis is approximately right (allows indexing) (53b635ce8)	CCTBX Commit via DLS Jenkins	Thu, 16 Mar 2017 14:03:44 +0000	94 lines
[git/cctbx] master: Don't re-refine after indexing by default when processing xtc streams. This mimics the behavior of dials.stills_process. (9a7f8613e)	CCTBX Commit via DLS Jenkins	Wed, 15 Mar 2017 16:50:30 -0700	78 lines
[git/cctbx] master: changes for creating cctbx zip bundle for Windows (544f8df47)	CCTBX Commit via DLS Jenkins	Wed, 15 Mar 2017 22:05:42 +0000	130 lines
[git/cctbx] master: Speeding up processing of anisotropic B-factors in mmCIF 10 times. (0d7c80dab)	CCTBX Commit via DLS Jenkins	Wed, 15 Mar 2017 11:32:09 -0700	198 lines
[git/cctbx] master: Format for SMV images with BEAMLINE=='TimePix_SU' (efe9758bf)	CCTBX Commit via DLS Jenkins	Wed, 15 Mar 2017 12:13:16 +0000	745 lines
[git/cctbx] master: another exception for FormatSMVADSC (82ad419f7)	CCTBX Commit via DLS Jenkins	Wed, 15 Mar 2017 12:13:16 +0000	79 lines
[git/cctbx] master: Fixed import of crystal model (f687d2911)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 16:14:16 -0700	79 lines
[git/cctbx] master: matched altloc identifiers in gui cbetadev to format for other validations (73cc39f2f)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 17:17:22 -0400	107 lines
[git/cctbx] master: added altloc identifiers to gui for suggested nqh flips (6787d18ab)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 17:11:52 -0400	76 lines
[git/cctbx] master: added altloc identifiers to gui for rama, rota, and omega (dfcf7dce6)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 17:07:46 -0400	144 lines
[git/cctbx] master: Updating bits for changes to dxtbx serialization (2ed7ebfe7)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 16:37:53 +0000	469 lines
[git/cctbx] master: Removed deprecated files and functions (fb8d85370)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 16:37:53 +0000	824 lines
[git/cctbx] master: Change for dxtbx serializde (cac0c247f)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 16:37:53 +0000	138 lines
[git/cctbx] master: Tidying up serialization stuff (890a26538)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 16:37:53 +0000	156 lines
[git/cctbx] master: fix test following dxtbx Crystal model changes (921892dac)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 16:17:19 +0000	98 lines
[git/cctbx] master: add to run_tests, thanks @phyy-nx for pointing this out (ae1c84aef)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 16:17:19 +0000	70 lines
[git/cctbx] master: rstbx/slip_viewer: store actions_menu object so it can be added to later (faf9b4853)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 16:12:27 +0000	175 lines
[git/cctbx] master: Attempt to identify dispatcher name if LIBTBX_DISPATCHER_NAME is not set. (899b29785)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 14:06:45 +0000	121 lines
[git/cctbx] master: Code to handle reading of compressed images; restores functionality which allowed dials to process gzip and bzip2 commpressed images & view in image viewer (70735fef7)	CCTBX Commit via DLS Jenkins	Tue, 14 Mar 2017 10:07:37 +0000	210 lines
[git/cctbx] master: IOTA v1.1.006 - GUI bugfixes to IOTA and PRIME (5d1b24cb9)	CCTBX Commit via DLS Jenkins	Mon, 13 Mar 2017 16:14:05 -0700	916 lines
[git/cctbx] master: Made pickling detector faster (460d24845)	CCTBX Commit via DLS Jenkins	Mon, 13 Mar 2017 17:03:46 +0000	446 lines
[git/cctbx] master: Added a deep copy function to detector (d44f78201)	CCTBX Commit via DLS Jenkins	Mon, 13 Mar 2017 12:03:32 +0000	264 lines
[git/cctbx] master: Removed old experiment list class and tidied up c++ boost pythnon definition. (258223b6d)	CCTBX Commit via DLS Jenkins	Mon, 13 Mar 2017 09:06:36 +0000	1109 lines
[git/cctbx] master: Moved Experiment class to C++ and moved dxtbx.model.experiment.experiment_list to dxtbx.model.experiment_list (8956eef4c)	CCTBX Commit via DLS Jenkins	Mon, 13 Mar 2017 09:06:36 +0000	1409 lines
[git/cctbx] master: Changed path to import Experiment and ExperimentList (793b8b308)	CCTBX Commit via DLS Jenkins	Mon, 13 Mar 2017 09:06:36 +0000	536 lines
[git/cctbx] master: Moved experiment list ot C++ (efe9f56e8)	CCTBX Commit via DLS Jenkins	Mon, 13 Mar 2017 09:06:36 +0000	81 lines
[git/cctbx] master: Major refactorization of eiger.py detector class relative to its initial implementation in 2013. Now rely exclusively on the dxtbx/format/FormatHDFEigerNearlyNexus class for HDF5 file I/O, while simply providing a thin wrapper here to adapt the data for the image viewer, labelit, and distl. (cd1711327)	CCTBX Commit via DLS Jenkins	Sat, 11 Mar 2017 18:49:04 -0800	584 lines
[git/cctbx] master: Minimum new code to support Eiger HDF5 files for distl.signal_strength. Use new range=[first, [last]] command line keyword to specify 0-based indices for the images to be analyzed. (47d03bf5c)	CCTBX Commit via DLS Jenkins	Sat, 11 Mar 2017 18:49:04 -0800	354 lines
[git/cctbx] master: Better value for beam center relevant for Labelit and Distl. (b1218e995)	CCTBX Commit via DLS Jenkins	Sat, 11 Mar 2017 18:49:04 -0800	87 lines
[git/cctbx] master: Change needed to support Labelit processing of HDF5 Eiger data. (25036db04)	CCTBX Commit via DLS Jenkins	Sat, 11 Mar 2017 18:49:04 -0800	75 lines
[git/cctbx] master: int2 (14e06c09c)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 20:16:07 -0800	97 lines
[git/cctbx] master: Minimal change in Format.py to assure that the _detectorbase_proxy has a vendortype attribute for use by the flex_image class. Developers can write new Format classes as long as they inherit from Format.py. All tests pass in dials_regression/test_viewer.py. (49954ded0)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 20:16:07 -0800	124 lines
[git/cctbx] master: int1 (d76ba0c06)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 20:16:06 -0800	152 lines
[git/cctbx] master: Another bugfix after dxtbx crystal changes (abcd759d3)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 15:50:34 -0800	98 lines
[git/cctbx] master: Simmple examples of refinement core, with or wihout data, xyz, adp. (ec8f49ceb)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 14:00:08 -0800	1647 lines
[git/cctbx] master: Enable removing some columns from a table before formatting it. (641c01a96)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 10:58:45 -0800	89 lines
[git/cctbx] master: Bugfix: integration pickles may not keep track of isoform. (f96b8bf44)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 10:55:55 -0800	82 lines
[git/cctbx] master: Bugfix: % accepted images relative to total instead of first bin. (b142d7c4a)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 10:43:52 -0800	106 lines
[git/cctbx] master: Adjust offset px mm mapping, now applied at readout, input should be provided in pixel shifts (13a069afc)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 14:31:39 +0000	212 lines
[git/cctbx] master: add color_scheme to FlexImage constructor (eliminates need for additional call to adjust when color_scheme != 0 (ec3cde7fc)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 09:46:58 +0000	669 lines
[git/cctbx] master: Get CBFlib from GitHub for new installations. (a33f51f0b)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 08:05:00 +0000	133 lines
[git/cctbx] master: update openssl to current LTS stable (c6c733689)	CCTBX Commit via DLS Jenkins	Fri, 10 Mar 2017 07:48:12 +0000	76 lines
[git/cctbx] master: Merge branch 'master' of ssh://github.com/cctbx/cctbx_project (8fb8f83ca)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 16:20:05 -0800	96 lines
[git/cctbx] master: Intermediate code to allow image_viewer display of Eiger HDF5 datasets with correct active area markup. Work still in progress. (202616432)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 16:19:39 -0800	133 lines
[git/cctbx] master: fix type (cfa0ef3de)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 14:34:13 -0800	72 lines
[git/cctbx] master: add mask out option (7acf9b46d)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 14:22:05 -0800	106 lines
[git/cctbx] master: IOTA v1.1.005 - minor bug-fix: imported time in Xterm IOTA (a3e942da5)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 13:47:36 -0800	94 lines
[git/cctbx] master: IOTA v1.1.005 - Input handling update (becfcadbd)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 13:26:12 -0800	118 lines
[git/cctbx] master: clean clutter (70bec6065)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 11:16:07 -0800	48 lines
[git/cctbx] master: Generalize active area definitions to Eiger-9M, -4M, -1M (3702baa62)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 11:16:07 -0800	277 lines
[git/cctbx] master: image_viewer: ensure color_scheme is persistent when changing images (8c41d51ef)	CCTBX Commit via DLS Jenkins	Thu, 9 Mar 2017 16:13:51 +0000	78 lines
[git/cctbx] master: Unbreak the identification of vendortype for the image viewer. For Dectris detectors this enables the visual identification of inactive areas and gets contrast levels correct. (e894e3671)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 22:50:32 -0800	191 lines
[git/cctbx] master: Example getter/setter with unit conversion. (2f6127676)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 22:50:32 -0800	114 lines
[git/cctbx] master: Determine active areas for Eiger. Image viewer shades these areas pink and omits them from contrast determining function. (d74f3e546)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 22:50:32 -0800	186 lines
[git/cctbx] master: Merge branch 'master' of ssh://github.com/cctbx/cctbx_project (6409b26d0)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 21:00:29 -0800	63 lines
[git/cctbx] master: Reconfiguration to assure that phil parameters for minimum_spot_area and minimum_signal_height for the EIGER operate correctly for both labelit indexing and distl.signal_strength, both as default parameters and as command line values. (5c230c7f6)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 20:59:54 -0800	146 lines
[git/cctbx] master: Separate EIGER defaults for signal_height (4.0) and spot_area (5). (888ddfcfc)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 20:59:53 -0800	121 lines
[git/cctbx] master: MolProbity GUI: change default xyz of validation residue objects from None to the mean of the residue coordinates; addresses issue where centering on an outlier will not work because xyz is None (4839e716e)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 16:19:28 -0800	163 lines
[git/cctbx] master: Sync with dxtbx interface changes to crystal model. Thanks Art for catching it. (8713b2a86)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 14:00:09 -0800	107 lines
[git/cctbx] master: more stats (a1c0bf8db)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 10:39:12 -0800	152 lines
[git/cctbx] master: iotbx.merging_statistics: optionally disable is_unique_set_under_symmetry check (6a300fb30)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 17:53:31 +0000	97 lines
[git/cctbx] master: add show_big_header to xtriage_output classes (b29f2a8c5)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 11:41:24 +0000	209 lines
Jenkins 5b cctbx MacOS build 968 Fixed	Jenkins Build Server (Diamond)	Wed, 8 Mar 2017 09:04:46 +0000	36 lines
[git/cctbx] master: import dependency to fix mac builds after dxtbx crystal model changes (76c2be61b)	CCTBX Commit via DLS Jenkins	Wed, 8 Mar 2017 08:54:22 +0000	100 lines
Jenkins 5a cctbx Tests build 3971 Fixed	Jenkins Build Server (Diamond)	Wed, 8 Mar 2017 06:14:33 +0000	37 lines
Jenkins 5a cctbx Tests build 3970 Unstable	Jenkins Build Server (Diamond)	Wed, 8 Mar 2017 03:01:15 +0000	100 lines
Jenkins 5a cctbx Tests build 3970 Unstable	Jenkins Build Server (Diamond)	Wed, 8 Mar 2017 03:01:15 +0000	36 lines
[git/cctbx] master: MolProbity GUI: multi-criterion plot does not display density graph when validating with a map file (4c0c6d2ff)	CCTBX Commit via DLS Jenkins	Tue, 7 Mar 2017 17:03:22 -0800	231 lines
[git/cctbx] master: MolProbity GUI: bug fix; map shifting modified coordinates in pdb_hierarchy, which made the GUI re-center in the wrong place (8ea15e32b)	CCTBX Commit via DLS Jenkins	Tue, 7 Mar 2017 15:58:44 -0800	233 lines
[git/cctbx] master: re-factor (2fbb8d412)	CCTBX Commit via DLS Jenkins	Tue, 7 Mar 2017 12:45:02 -0800	167 lines
Jenkins 5b cctbx MacOS build 965 Unstable	Jenkins Build Server (Diamond)	Tue, 7 Mar 2017 15:41:12 +0000	249 lines
[git/cctbx] master: Added a check for mosaicity = NOne (0caa8929a)	CCTBX Commit via DLS Jenkins	Tue, 7 Mar 2017 15:27:49 +0000	75 lines
[git/cctbx] master: Moved old crystal model code to tests to ensure same results and added fix for similarity check (60ef166c8)	CCTBX Commit via DLS Jenkins	Tue, 7 Mar 2017 14:51:38 +0000	2252 lines
[git/cctbx] master: Added the C++ files for the crystal model (66471e519)	CCTBX Commit via DLS Jenkins	Tue, 7 Mar 2017 14:29:54 +0000	2652 lines
[git/cctbx] master: 1. Moved the crystal model to C++ 2. Renamed crystal_model -> Crystal to make more consistent with other dxtbx models 3. get_A() etc now returns mat3 which maps to tuple in python, therefore needed to fix places which assume a scitbx.matrix (975f50250)	CCTBX Commit via DLS Jenkins	Tue, 7 Mar 2017 14:28:08 +0000	1857 lines
[git/cctbx] master: Assed "inline" to function spec to allow use in multiple places without getting multiple definition error (82750ac77)	CCTBX Commit via DLS Jenkins	Tue, 7 Mar 2017 14:26:35 +0000	76 lines
[git/cctbx] master: Refactor codes, report indexing choices. (f159b22ea)	CCTBX Commit via DLS Jenkins	Mon, 6 Mar 2017 18:57:38 -0800	1298 lines
[git/cctbx] master: Bug fix in expand_to_p1, and a test. (9b7693978)	CCTBX Commit via DLS Jenkins	Mon, 6 Mar 2017 16:05:36 -0800	174 lines
[git/cctbx] master: Introduce CCbox, CCimage, CCmask, CCvolume, CCpeaks. Efficeint calculation of CC in reciprocal space. Introduce alternative to FSC-derive resolution: d99. Bug fix in assertin in bss. Misc changes. (df28ada29)	CCTBX Commit via DLS Jenkins	Mon, 6 Mar 2017 16:05:36 -0800	2838 lines
[git/cctbx] master: MolProbity GUI: bug fix for multicriterion plot; y-limits were not correct due to numpy NaN values (1e1a44b4d)	CCTBX Commit via DLS Jenkins	Mon, 6 Mar 2017 13:52:13 -0800	80 lines
[git/cctbx] master: Plot all detectors found in json file in dxtbx.plot_detector_models (d84b569fe)	CCTBX Commit via DLS Jenkins	Mon, 6 Mar 2017 13:01:14 -0800	94 lines
[git/cctbx] master: Bugfix. Another leftover from the workshop. (8940a58b3)	CCTBX Commit via DLS Jenkins	Mon, 6 Mar 2017 13:01:14 -0800	83 lines
[git/cctbx] master: More available info for scripting. Params for hbonds cutoffs. (eb8257e3f)	CCTBX Commit via DLS Jenkins	Mon, 6 Mar 2017 11:34:48 -0800	412 lines
[git/cctbx] master: MolProbity: remove random print statement (bc0141432)	CCTBX Commit via DLS Jenkins	Mon, 6 Mar 2017 10:46:18 -0800	75 lines
[git/cctbx] master: Relaxed criteria for forcing rama outlier corrections. Splitting ccd_is_ok function into two for use separately. (a2f7a2850)	CCTBX Commit via DLS Jenkins	Fri, 3 Mar 2017 16:48:03 -0800	548 lines
[git/cctbx] master: MolProbity: added default argument for optional parameter when doing real-space correlations (e1e08e3c9)	CCTBX Commit via DLS Jenkins	Fri, 3 Mar 2017 16:12:10 -0800	82 lines
[git/cctbx] master: MolProbity: change real-space correlation to use mmtbx/command_line/map_model_cc.py for maps (48628a972)	CCTBX Commit via DLS Jenkins	Fri, 3 Mar 2017 15:32:13 -0800	503 lines
[git/cctbx] master: Inrease speed of list comparison by doing list->set conversion before check (2b5e49548)	CCTBX Commit via DLS Jenkins	Fri, 3 Mar 2017 14:05:12 -0800	169 lines
[git/cctbx] master: Do not autosharpen with really bad model (f90a452cf)	CCTBX Commit via DLS Jenkins	Fri, 3 Mar 2017 12:33:16 -0700	120 lines
[git/cctbx] master: catch case that H atom does not have bond proxie (b894bd121)	CCTBX Commit via DLS Jenkins	Fri, 3 Mar 2017 11:24:12 -0800	403 lines
[git/cctbx] master: bugfixes to ramalyze to calculate omega dihedral correctly for proline (21589c496)	CCTBX Commit via DLS Jenkins	Thu, 2 Mar 2017 16:27:20 -0500	96 lines
[git/cctbx] master: Bugfix: print cs summary after determining cs for GUI (c8a79bd57)	CCTBX Commit via DLS Jenkins	Thu, 2 Mar 2017 10:56:31 -0800	97 lines
[git/cctbx] master: some more diagnostics for parameterization (5ec2e48bf)	CCTBX Commit via DLS Jenkins	Thu, 2 Mar 2017 09:45:58 -0800	151 lines
[git/cctbx] master: Allow user to set k_sol, b_sol. (4d97a720c)	CCTBX Commit via DLS Jenkins	Wed, 1 Mar 2017 18:10:59 -0700	326 lines
[git/cctbx] master: Add default k_iso b_iso in model-based sharpening (4670668e4)	CCTBX Commit via DLS Jenkins	Wed, 1 Mar 2017 17:56:44 -0700	120 lines
[git/cctbx] master: update auto_sharpening to skip normalization of model map in model-based sharpening (7b3be12a0)	CCTBX Commit via DLS Jenkins	Wed, 1 Mar 2017 17:33:54 -0700	186 lines
[git/cctbx] master: Function to select rama allowed, used in map preparation. Join neighbour outliers. Do not accept exactly the same CCD solution that was used in previous iteration. Choosing another rama angle for additional CCDs Rejecting the same solutions. Filter out previously tried angles before doing CCD. returning weight calculations back to normal. (d32fd6a69)	CCTBX Commit via DLS Jenkins	Wed, 1 Mar 2017 11:00:07 -0800	1832 lines
[git/cctbx] master: moved stderr to buffer to avoid t6 "WARNING" (e93fc5136)	CCTBX Commit via DLS Jenkins	Tue, 28 Feb 2017 14:21:52 -0800	123 lines
[git/cctbx] master: Merge branch 'master' of github.com:cctbx/cctbx_project (f5ddeb336)	CCTBX Commit via DLS Jenkins	Tue, 28 Feb 2017 14:12:18 -0800	231 lines
[git/cctbx] master: Damp shifts in one of real-space refinement engines. (54fbe7328)	CCTBX Commit via DLS Jenkins	Tue, 28 Feb 2017 14:12:11 -0800	269 lines
[git/cctbx] master: Need to add requests for Amber download script. (60ca28167)	CCTBX Commit via DLS Jenkins	Tue, 28 Feb 2017 13:47:29 -0800	98 lines

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