Advanced Tab

This tab provides additional optional features for Rosetta to calculate the result models.

_images/advanced_tab_symmetry.png

Symmetry

This box requires a run of the external symmetry detection tool as provided in the Symmetry tab. The information in this section will be used during execution script generation.

  • Use SYMM file: Enabling this check box will also enable Rosetta to use use the provided symmetry file.

  • HELIX: Enable this check box if helical symmetry is used. It will not add the flag -score_symm_complex to the Rosetta execution as done for normal symmetry.

  • Select: When the symmetry detection in the Symmetry tab was sucessful, the correct symmetry file name and location will be preset. Alternatively a external .symm file can be selected here.

Model evaluation

This box is used for to enable Rosetta to evaluate the results by the given model.

  • Use independent map for validation (half2): Enable this check box if two filtered half-maps are used.

  • Select: The second .pdb half-map file can be selected here.

Constraints

Supply additional constraints for atom-atom distances for the Rosetta execution.

Sets

  • Use constraint set from file: Enables the use of an constraint file. An example constraint file entry would be like:

    AtomPair CA 131 CA 171  BOUNDED 0.0 5.0 1 X

  • Select: Select a constraint file generated by hand or another software. The file suffix should be .cst.

Versions

The density weights database is distributed with Rosetta and there are various versions depending on the used Rosetta version.

  • Rosetta 3.8 or below: The talaris2013 database can be used when the parameter -restore_talaris_behavior is added to the Rosetta command line executable as additional parameter e.g. in the StarMap bash template.

  • Rosetta 3.9 or higher: ref2015 is the default.