Define Structural ROIs

This protocol allows the user to manually define a SetOfStructROIs from AtomStruct objects. The user can define this structural ROIs in different ways:

  • Coordinates: directly specify the coordinates of the ROI over the structure.

  • Residues: specify those residues in the protein structure that are ROIs.

  • Ligands: existing ligands in the input structure or external (from another input) small molecules docked to the same structure.

  • Protein-Protein Interfaces: specify the interface of a pair of chains in the structure.

  • Near Residues: specify a pattern of residues that have to exist nearby.

The list of input ROI definitions are mapped to actual coordinates, which can optionally be mapped to the protein surface. These resulting points are clustered to yield the final structural ROIs.

Input

Note

All parameters include a help button that gives further information for each of them.

Define Structural ROIs form

The result of this protocol is a SetOfStructROIs containing those regions listed in the form.

Define Structural ROIs output

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests pwchem.tests.tests_structROIs.TestDefineStructROIs