Options is the fourth screen of the Protein Design wizard.

Enter the substitution variations you wish to model.

  • Repack neighbors – When this box is checked, as it is by default, the residues in contact with the variant positions are also repacked during modeling. This can help better accommodate changes occurring at selected positions.
  • Allow backbone flexibility with backrub motion – When this box is checked (it is unchecked by default), the backbone atoms at the selected positions are allowed to move using the “backrub” algorithm. This allows sampling local backbone plasticity in a realistic manner (reference).

The following two options are only visible if you selected Search for variants that improve folding stability (early release) in the Workflow screen:

  • Maximum sequences to report – In the box, specify the maximum number of new sequences to report from the search. Sequences are ranked by lowest energy.
  • Energy cutoff from global minimum – In the box, specify an energy threshold value. Sequences whose energy is higher than that of the lowest-energy sequence PLUS this threshold value will be excluded from the list of results.

To learn about the optional tools in the bottom left corner of the screen, see the bottom of this topic.

Once you have made the desired selections, continue by doing one of the following:

  • To specify additional options, press Next to continue to the Job screen.
  • To return to a previous screen, press Back.
  • To close the Protein Design wizard without starting a search, press Cancel.

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