Back to Mover page.
Documentation created by Vikram K. Mulligan, Baker laboratory. For questions, e-mail vmullig@uw.edu. 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:
<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>