Table 1.
Function Types Typically Used in Constraints to Penalize Structural Models in CS-Rosetta
| Bounded |
| Format: |
| AmbiguousNMRDistance atom1_label atom1_residue_no atom2_label atom2_residue_no BOUNDED lb ub sd annotation |
| Example: |
| AmbiguousNMRDistance H 185 QD2 175 BOUNDED 1.5 4.20 1.000 automatic NOE Peak |
| AmbiguousNMRDistance H18H23 BOUNDED 1.5 3.40 1.000 automatic NOE Peak |
| Sigmoid |
| Format: |
| AtomPair atom1_label atom1_residue_no atom2_label atom2_residue_no SIGMOID center slope annotation |
| Example: |
| AtomPair CB38 CB56 SIGMOID 8.00 1.00 #ContactMap: 1.35 |
| AtomPair CB 118 CB 165 SIGMOID 8.00 1.00 #ContactMap: 1.22 |
| SOGFUNC |
| Format: |
| AtomPair atom1_label atom1_residue_no atom2_label atom2_residue_no SOGFUNC no_of_functions mean1 sd1 wt1 … |
| Example: |
| AtomPair CA 4 CA 23 SOGFUNC 2 8.980 2.897 0.265 18.300 7.300 0.735 |
| AtomPair CA 8 CA 47 SOGFUNC 1 7.842 2.297 0.312 |
center, center of the SIGMOID function; lb, lower bound; sd, standard deviation; slope, slope of the SIGMOID function; ub, upper bound; wt, weight.
Rosetta provides a large set of function types, here we show only some examples of a representative subset used by CS-Rosetta (https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file).