Back to Mover page.
Documentation created by Vikram K. Mulligan, Baker laboratory. For questions, e-mail firstname.lastname@example.org. Last updated 24 October 2015.
Kinematic closure is a computationally-inexpensive, analytical algorithm for loop closure. Given a loop with defined start- and endpoints, with N degrees of freedom, it is possible to sample N-6 of these degrees of freedom and to solve for the remaining 6. GeneralizedKIC is a generalization of the classic KIC algorithm that permits closure and conformational sampling of any covalently-connected chain of atoms. Chains to be closed can include backbone segments, covalently-linked side-chains (e.g. disulfide bonds), ligands, noncanonical residues, etc. GeneralizedKIC is invoked in RosettaScripts as follows:
See the GeneralizedKIC documentation for details about GeneralizedKIC options, and about GeneralizedKIC perturbers, filters, and selectors, as well as for usage examples. Note: GeneralizedKIC should currently be considered a "beta" feature. Some details of the implementation are likely to change.
<GeneralizedKIC name="(string)" closure_attempts="(2000,int)" stop_if_no_solution="(0,int)" stop_when_n_solutions_found="(0,int)" selector="(string)" selector_scorefunction="(string)" selector_kbt="(1.0,Real)" contingent_filter="(string)" correct_polymer_dependent_atoms="(false,bool)"> #Define loop residues in order: <AddResidue res_index="(int)"/> <AddResidue res_index="(int)"/> <AddResidue res_index="(int)"/> ... #List tail residues in any order (see documentation for details): <AddTailResidue res_index="(int)"/> <AddTailResidue res_index="(int)"/> <AddTailResidue res_index="(int)"/> ... #Pivot atoms are flanked by dihedrals that the KIC algorithm will solve for in order to enforce closure: <SetPivots res1="(int)" atom1="(string)" res2="(int)" atom2="(string)" res3="(int)" atom3="(string)" /> #One or more perturbers may be specified to sample loop conformations: <AddPerturber effect="(string)"> ... </AddPerturber> ... #One or more filters may be specified to discard unwanted or bad closure solutions: <AddFilter type="(string)"> ... </AddFilter> ... </GeneralizedKIC>