Merge pull request #1596 from RosettaCommons/roccomoretti/relax_centroid_native
Fix issue with centroid poses and -relax:constrain_relax_to_native_coords
-relax:constrain_relax_to_native_coords would only work if you also included the -in:file:fullatom flag. Otherwise, the native pose would get loaded as centroid mode. (By set_native_in_mover() in src/protocols/jd2/util.cc)
That's terribly silly, as relax is a full-atom only protocol. (Doubly so, as the -s gets loaded as fullatom by default, but the -in:file:native is loaded as centroid.)
This pull request bypasses the "is it centroid or not" logic, and always loads the native reference pose as fullatom.
Integration test changes expected in relax_w_allatom_cst, as the native pose is now loaded as centroid (due to removing the -in:file:fullatom flag from the integration test), even though the centroid version is not used.
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Merge pull request #1581 from RosettaCommons/jadolfbr/grafting_disulfides
Fix antibody.cc
This PR adds an option, optimal_graft, that fixes the grafting component of antibody.cc. By fix, I mean that it uses the exact settings we have successfully used for antibody design - this results in 100% graft closure, clean disulfides, and lower energies. By using other code for this option, we also fix a major bug in the grafting component of antibody.cc, which is responsible for much of the disulfide issues.
We also add disulfide score terms for centroid mode in AnchoredGraftMover's default, smooth centroid score function. They help to lessen the effects of the bug without the optimal_graft option, but do not alleviate it completely.
This will change a few integration tests that use AnchoredGraftMover or CCDEndsGraftMover including antibody_designer and AnchoredPDBCreator due to the additional centroid score terms.
Thanks to @lqtza for testing and debugging all this with me, as well as the work calling Relax directly for the final relax, instead of generating it from cmd-line options.
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Merge pull request #1546 from RosettaCommons/jadolfbr/ab_numbering_converter
Antibody numbering conversion
Description
=========
* Add a mover and app for converting antibody structures from one numbering scheme to another.
* Change numbering_scheme option to input_ab_scheme
* Implement output_ab_scheme to every app that outputs antibodies, so users can use any scheme as input and get any scheme as output in antibody apps, including antibody.cc (well, at least for output).
*Fix public app code_template.
- [x] Add Mover to inter-convert numbering schemes: ```AntibodyNumberingConverterMover```
- [x] Add app that does the conversion: ```antibody_numbering_converter```
- [x] Add integration test for app
- [x] Add RosettaScript Integration
- [x] Test with structures numbered in AHo and convert to Chothia! Woohoo! Reload the Chothia antibody in Rosetta, test clustering, CDRs, etc.
- [x] Update intra-cdr numbering database file manually using 2001 AHo numbering paper and the numbering scheme atlas.
- [x] Test crazy H3 antibodies and thoroughly write unit tests to interconvert all schemes and load back in.
Requested:
=========
- [x] Change input flag from ```-numbering_scheme_``` to``` _-input_ab_numbering_```
- [x] Change output flag from ```-output_numbering_scheme``` to ```-output_ab_numbering```.
- [x] Remove ```_Scheme``` suffix for numbering schemes - at least in terms of string parsing.
Current Use
=========
Just add the option, ```-output_ab_scheme``` to any antibody app that writes PDBs or the converter app.
Note that the option ```-input_ab_scheme``` instructs which numbering scheme the current input pdb is (and that ```-numbering_scheme``` option has been deprecated in favor of this option).
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Merge pull request #1549 from RosettaCommons/everyday847/rna_thread_and_minimize
No integration test changes (save what's expected, e.g. number_of_residuetypes)
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Updating the Xcode project template file to be compatible with the
libxml2 in external.
Xcode users: you will need to remove the project file and regenerate it
using the following command:
$ cd Rosetta/main/source/xcode && rm Rosetta.xcodeproj/project.pbxproj
&& python make_project.py all
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Merge pull request #1568 from RosettaCommons/everyday847/better_ERRASER_minimization
All of you who really love refining RNA structures: the first stage of doing so just got a lot faster!
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