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Application created by Roland Pache. The corresponding principal investigator is Tanja Kortemme (kortemme@cgl.ucsf.edu).

Purpose

When creating a resfile for design positions, it's often useful to allow residues around the design positions to repack to accommodate the new amino acid identities. Manually identifying and specifying these residues can be tedious. The create_clash-based_repack_shell application aims to simplify this.

This application takes an input structure and a resfile with designable positions, and then automatically locates those positions with sidechains which may clash with any of the designable residues. It then alters the resfile to add repacking to those positions.

Input Files

  • -in:file:s -- The input protein to be designed. Note that currently the application will only use a single PDB-formatted file passed to -in:file:s -- other input approaches/formats do not work.
  • -packing:resfile -- The initial resfile to use. This resfile should specify one or more positions to design. (The application may not work correctly with a repack-only resfile.) Other positions may be either NATAA or NATRO.

Output

The file specified with -packing:resfile will be modified by adding NATAA lines for each (non-design) residue in the protein which has a sidechain which may clash with any of the designable rotamers at any of the designable positions.

A list of these residues will be printed to the tracer output, along with a PyMol-formatted selection string which can be used to visualize the locations of the selected residues.

See Also