commit c0e92cf87b5ca6480bd8530e168e3ac3d3566e29
Date:   Thu Sep 17 15:13:40 2015 -0700

    goes with previous commit: fix possible bug in stepwise minimizer, setting of working_minimize_res

commit 5c0891e5ccc724778e0e95d7f032345c82336c0d
Date:   Thu Sep 17 14:57:46 2015 -0700

    fix possible bug in stepwise minimizer, setting of working_minimize_res

commit edd9836c1d021bf7c5dc1fc7774478aa7730f2b8
Merge: 28c6ff8 7a0c336
Date:   Thu Sep 17 03:13:35 2015 -0700

    Merge pull request #805 from RosettaCommons/vmullig/genkic_minsolutions_bug
    
    Caught a bug in GenKIC.
    
    Expect GenKIC integration test changes.

commit 28c6ff884d5ee7a3d08bee1b2ea812dcde41f67b
Merge: 2e802cd 6f8f90b
Date:   Wed Sep 16 15:57:57 2015 -0600

    Merge pull request #802 from RosettaCommons/benchmark
    
    Adding options to benchmark scripts for PyRosetta debug releases

commit 2e802cd97b75228fcdb792ac7fb45c1130a44b7c
Merge: 00ea033 ff1989e
Date:   Wed Sep 16 13:17:35 2015 -0700

    Merge pull request #796 from RosettaCommons/tlinsky/tlinsky/rcg_remove_exception
    
        RemodelConstraintGenerator now throws exception when constraints can't be removed

commit 00ea0333284dbec7b1be4c348ffec0fa8f069275
Merge: 4b45f17 b1614e0
Date:   Wed Sep 16 10:48:06 2015 -0400

    Merge pull request #797 from RosettaCommons/JWLabonte/patch_system
    
    Patch system: Adding PatchOperation for changing a bond type
    
    All tests pass, except for broken/unstable integration tests.

commit 4b45f173ea141bfc1aedef7fbefb6c73765c9a7a
Merge: df73fb2 1bf137d
Date:   Tue Sep 15 14:07:45 2015 -0700

    Merge pull request #800 from RosettaCommons/dougrenfrew/2-amino-octanoic_acid
    
    Adding 2-amino-octanoic acid the l-ncaa residue types. The `number_of_residuetypes` integration test expected to fail.

commit df73fb2c17bff247c11ac1e3f25b23d18568b436
Merge: 29f0d66 a9c9dc6
Date:   Mon Sep 14 15:42:36 2015 -0700

    Merging with remote

commit 29f0d66f11380e05d5640a7c5bb5b619d5891174
Date:   Mon Sep 14 15:32:43 2015 -0700

    Removed the new lines in the fold tree silent file output format. The fold tree
    should be output into a single line in the silent file.

commit bcc1a5fb03a6fb9b6974cc241156a710cd6738cd
Date:   Mon Sep 14 14:22:14 2015 -0400

    silencing cpp complaint

commit 7ab62678154ca8a38b59a5d6cde9bd193611da24
Merge: d36ef3b 8f698fd
Date:   Sun Sep 13 17:42:45 2015 -0400

    Merge pull request #731 from RosettaCommons/JWLabonte/sugars/general
    
    Carbohydrates: Refactoring CarbohydrateInfo to use singleton for static const data
    
    Unit tests pass.
    carbohydrate test changes expected because of expanded Gasteiger testing. All other integration test failures are from broken/unstable tests.
    cpp test change is not a true case.

commit d36ef3b0951f257ca5ee3bbd5f8ba5ca2b54bbd7
Merge: 7d5728d e246c34
Date:   Sat Sep 12 03:36:30 2015 -0700

    Merge pull request #792 from RosettaCommons/vmullig/better_error
    
    Adding a more explicit error message to replace the seqpos <= size error, which didn't mean much to users.

commit 7d5728df0a38331c635e0eb3c3546352d6cece84
Date:   Fri Sep 11 17:44:42 2015 -0700

    Fix another patch pair incompatability

commit 55371edb3ccd0d9d94ab36f95b814a74fb7e4bf3
Date:   Fri Sep 11 17:13:19 2015 -0700

    Remove unused vars from some pilot apps.  Small bugfix with endian check for binary silent structs.

commit db3c9b310f177b8bcbe41e8f5d5df627d5a36dee
Merge: 1c47382 36f5c42
Date:   Fri Sep 11 14:58:19 2015 -0700

    Merge pull request #790 from RosettaCommons/vmullig/layerdes_defaults
    
    Making use_symmetry=true the default LayerDesign behaviour.
    
    Previously, the default behaviour was to extract the asymmetric unit and only use this when setting up layers. Now, the whole, symmetric pose is used by default. The user can override this by setting use_symmetry=false in RosettaScripts.

commit 1c473825cc6e6f6aef6f91d58ab532d46fd35191
Merge: 3a94651 40efd66
Date:   Fri Sep 11 17:14:25 2015 -0400

    Merge pull request #779 from RosettaCommons/axial_equatorial/main
    
    ÆRIS-Project
    
    All unit tests pass.
    carbohydrate, fiber_diffraction, and fold_and_dock integration test changes expected because of output changes.
    code_duplication is because of moving code.
    dna_interface, mm_params, pna, inverse_rotamer_remodel, and match tests are broken and/or unstable.

commit 3a94651a8770220f83f40aee5481e5f57bc970eb
Merge: 362feb0 661920d
Date:   Fri Sep 11 13:53:58 2015 -0700

    Merge pull request #786 from RosettaCommons/calebgeniesse/erraser-fix
    
    ERRASER Performance Restoration

commit 362feb0b45c5f4470332718af9f6f69aa42451e1
Merge: 659c167 5a4f5f9
Date:   Fri Sep 11 12:58:05 2015 -0700

    Merge pull request #787 from RosettaCommons/tlinsky/matcher_multiplepose
    
    Make MatcherMover a MultiplePoseMover

commit 659c1678648af371849932e62290c62d0cb15bb7
Date:   Thu Sep 10 18:00:37 2015 -0700

    Bugfix for localreax + symmetry

commit 142cfcc0db152bce7472b0eadf68de8645259c26
Merge: 5c867ce 7fb799d
Date:   Thu Sep 10 14:54:04 2015 -0700

    Merge pull request #785 from RosettaCommons/vmullig/symm_layerdes
    
    Allow LayerDesign to use symmetry
    
    Currently, LayerDesign extracts the asymmetric unit of a symmetric pose, and uses that to define core, boundary, and surface layers.  This adds an option to use the whole symmetric pose.
    
    Tasks:
    - [x] Add "use_symmetry" option.
    - [x] Have the option alter LayerDesign's behaviour.
    - [x] Integration test.
    - [x] Documentation.
    - [x] Beauty.
    - [x] Also, pulling in a minor change to core::conformation::parameters::ParametersSet.hh.  (It's something that will have to be tweaked when I fix the ResidueOP issue, and I want it in master so that I remember to do this, rather than in the branch where I added the functions, where the functions will be broken by a fix in master.)

commit 5c867ceeccf50fc7553ab89f5d2f20cafe791052
Merge: b6031890 e76c07a
Date:   Thu Sep 10 09:40:40 2015 -0700

    Merge pull request #782 from RosettaCommons/dimaio/denovo_density_fixes
    
    This pull requests add the de novo cryoEM model-building tools described from Wang et al. 2015 to public apps.
    
    It introduces the new public app, 'denovo_density'. Additionally, it makes a few bugfixes to the spherical harmonic code, and introduces a new mover, electron_density/DockIntoDensity, a general mover for matching proteins structures to density maps through fast 6D search.
    
    Additionally, several other miscellaneous fixes for modelling into cryoEM density are added in this checkin. This includes a number of accumulated bugfixes and new features to RosettaCM.

commit b60318904de3a2e79030ad7ce6b9c4998f3b2c0a
Merge: d49cb29 a6ce7e2
Date:   Thu Sep 10 10:42:26 2015 -0500

    Merge pull request #735 from RosettaCommons/roccomoretti/gasteiger_SO4
    
    Gasteiger atom typing updates
    
    We weren't appropriately handling some of the "stranger" ways of specifying certain functional groups. Add fixes and unit tests, and add an "allow_unknown" option for Gasteiger atom typing, so it doesn't crash on difficult typing.
    
    Integration test changes in "carbohydrates" expected, as we're now special-casing the N-terminus of amino acids to get the correct typing.

commit d49cb29f069c636bfa902537d36ffecc1a6d5554
Date:   Wed Sep 9 16:48:52 2015 -0400

    PNA integration test flags file typo

commit 64e1e38d7cf5efe521486bbe6e59609546dc77ea
Date:   Wed Sep 9 11:05:03 2015 -0400

    Adding updated MARCC settings file. No test changes expected.

commit f411ebf7e8a5c74bb08dc9db51d26d993842cae1
Merge: 3a2ede0 372918e
Date:   Wed Sep 9 11:03:26 2015 -0400

    Merging current copy of master

commit 3a2ede01e01c6353b4570529ea3710f8d5b24191
Date:   Tue Sep 8 12:20:51 2015 -0400

    Adding the MARCC site settings file

commit f0c4db43f145161ca625ff34dd3213d5fb515bb9
Merge: 2c1d760 9b22bb5
Date:   Tue Sep 8 12:17:43 2015 -0400

    Pulling from remote master

commit 2c1d7605449c25234cc1f1c3bf863ea264bbd1fe
Date:   Mon Jun 8 14:44:52 2015 -0400

    Minor change to adding_peptoids app