Merge pull request #1044 from RosettaCommons/rfalford12/step0_benchmarks
Helix Tilt Angle Benchmark
Movers & RosettaScripts for calculating the tilt angles of single trans-membrane spanning helices in the bilayer:
In protocols/membrane/benchmark:
MakeCanonicalhelix: Given a pose extended from sequence (using ExtendPoseMover) create a canonical alpha-helix using ideal helix dihedral angles (phi = -47 degrees, psi = -57 degrees, omega = 175 degrees ) from an optional start to end point.
SampleTiltAngles: Given a single transmembrane spanning helix, calculate the energy vs. helix tilt angle and compare the energies from multiple scoring functions
New Tests
Unit test for MakeCanonicalHelix
Integration test for SampleTiltAngles (based on RosettaScripts)
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Merge pull request #1069 from RosettaCommons/tlinsky/taskselector
Add residue selector to select based on a task operation
task_selector integration test is new
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Allow BuildPeptide to build helical, not just extended, peptides
New boolean -helix option.
More generally, there are real-valued -phi and -psi options,
which allow you to specify the values you want repeated.
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Merge pull request #768 from RosettaCommons/possu@u.washington.edu/repeat_update
updates to remodel to include repeat protein building features
1) Remodel repeat features
2) improved symmetry handling in repeats
3) change default chain behavior to A
4) change CCDclosure mover output levels (it's otherwise hard to use the output)
integration test changes: almost all are cosmetic from changing the output levels of CCD closure mover. Remodel related test changes are expected.
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Merge pull request #1068 from RosettaCommons/smlewis/temp_partly_disable_AnchorFinder_itest
disabling 3cy0, 3cy1, 3cy5 in AnchorFinder itest. They have cys-heme…
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Merge pull request #1062 from RosettaCommons/xrw_use_pdb_components
Enable loading of PDB components
This commit is part of the XRW effort, and enables loading of residue type definitions from the provided chemical components dictionary. To use, download the Chemical Components Dictionary components.cif (or components.cif.gz) from http://www.wwpdb.org/data/ccd to Rosetta/main/database/chemical/, and then pass the flag -load_PDB_components on the commandline. For the current version, you will also want the -ignore_waters flag, as water is one of the components. (This may be altered at some point, with the new PDB file reading code.)
If Rosetta encounters a residue three letter code that it doesn't know, it will look in the chemical components dictionary for the definition, and create a corresponding ResidueType. It will also attempt loading in situations where the name3 may be ambiguous, and use the standard atom-name based resolution to pick the best match. If you have a ligand whose chemical identity does not match a PDB-standard residue, you will still need to provide the definition for the ResidueType yourself.
Known limitations are that any ResidueType loaded from the Chemical Components Dictionary will be loaded as an independent, non-polymeric ligand. The ResidueTypes are also made as the PDB provides them, which may not match the tautomeric/protonation state you expect. Additionally, no rotamers are generated for these residues. The PDB components are also not loaded for centroid-mode poses. Certain three letter codes and poses may still have issues loading correctly. (This will be partially fixed by other XRW commits.)
A number of cosmetic integration test changes are expected. (Mostly extra information printout.) (cf http://benchmark.graylab.jhu.edu/revision?id=3317&branch= and http://benchmark.graylab.jhu.edu/revision?id=3321&branch=) This branch also contains some fixes for PyRosetta and the external/cifparse library.
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Merge pull request #1063 from RosettaCommons/sacombs/check_UFF_atom_types
Add UFF-based atom types for more elements
This commit adds most elements to the full atom atom type set. The LJ parameters are derived from the UFF force field. The LK parameters are based on the approach already used for halogen and metal ions in Rosetta. (i.e. arbitrary guesses)
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