Rosetta Tab

This tab provides the starting point for the most commonly used Rosetta refinements. It is divided in two sections. First, the selected input data must be saved in ChimeraX or selected from the filesystem. Second, the choosen Rosetta strategy and additional settings must selected before saving and executing the analysis.

_images/rosetta_tab.png

ChimeraX

Select your used atoms for refinement in ChimeraX e.g. the following example selects chain A,B,C and F in model 1::

sel #1 /A-C,F
  • PDB file (selected atoms only): Choose the selected atoms for further analysis.

  • Save: Once the atoms are selected they must be saved in a PDB file by pressing this button and choosing a file name with the extension .pdb. If nothing was selected a simple basic pdb file will be generated. This command uses the ChimeraX save command e.g. save chainA.pdb selectedOnly true.

  • Select: Alternatively a previous saved .pdb file can be selected here. This file will not be opened in ChimeraX.

Strategy

The choosen strategy is important for the expected results and comes with two selection possibilities in the StarMap user interface. First a rebuilding or refinement strategy and second the used residues of the dataset can be choosen.

  • Strategy: Can be Full rebuild, Minimal rebuild, Refinement only (cartesian refine) and Torsian refine.

    • Full rebuild: Perform multiple iterations of backbone sampling followed by side-chain rebuilding and all-atom refinement.

    • Minimal rebuild: Full rebuild, but only one iteration is performed.

    • Refinement only: Perform side-chain rebuilding and all-atom refinement in Cartesian space. Only run cartesian or torsian model refinement, do not rebuild backbone residues. This approach is particulary useful for maps with worse than ~5A resolution.

    • Torsian refine: Perform side-chain rebuilding and all-atom refinement in torsian (“internal coordiante”) space. This approach is useful for models with large domain motions where the resolution is too low for the Full rebuild to converge. Recommened for maps worse than ~5A resolution.

    All these rebuilding and refinement strategies can be combined with automatic or user defined residues.
    • auto: Detect and rebuild poorly modelled regions by analyzing the Ramachandran score, bond lengths and angles as well as fit into the density.

    • user, Residues in selection: Provide a comma-seperated list of short residue specifications to be refined. Each value can be in a range e.g. 22A-36A,56B-77B.

Results

  • Number of output models: Set the number of output models, i.e. how many PDB files will be generated as result files. Each output model is calculated independently by a Rosetta process using one computing core. MPI-enabled Rosetta (see Rosetta best practice) can calculate output models in parallel at one or more computing nodes. The StarMap user interface suggests and presets useful values for the chosen Strategy. By default, Full rebuild generates 20 output models, Minimal rebuild generates 10, while Minimal refinement and Torsion refinement default to 1.

Resolution

  • Map Resolution: The density map resolution. Should be the same value as used later in the Analysis tab. Enter the value and press the Return or Tab button to update the value in both entry fields.

Density

  • Densitiy map (full or half1): Choose a full density map or one of the two half maps for analysis. The path and filename will be used in the execution script of Rosetta.

  • Select: The .mrc map file can be selected here.