CreatePredAlphaCost pred_alpha2k alpha11 T0372.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0372.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0372.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 30 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 30 backbone_clashes 2 \ break 200 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 50 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ missing_atoms 1 \ maybe_metal 0.5 \ maybe_ssbond 1 \ known_ssbond 0.5 \ // remove maybe_ssbond weight if protein known to be in reducing environment. // remove maybe_metal weight if protein known to have disulfides or // known not to bind metal ions. // Add the following for extra-cellular proteins: # and put ssbond command in constraints file // For comparative modeling, increase weight of break and hbond_geom... // put any constraints here, such as helix constraints, strand constraints, // sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms. SSBOND C176 C181 include decoys/try8-opt2.helices SheetConstraint (T0372)T43 (T0372)I48 (T0372)F56 (T0372)F51 hbond (T0372)I48 1 SheetConstraint (T0372)V53 (T0372)A58 (T0372)M66 (T0372)Q61 hbond (T0372)F54 5 SheetConstraint (T0372)T207 (T0372)N214 (T0372)M224 (T0372)I217 hbond (T0372)G208 1 SheetConstraint (T0372)A219 (T0372)I226 (T0372)K237 (T0372)T230 hbond (T0372)F222 4 SheetConstraint (T0372)L62 (T0372)P67 (T0372)N90 (T0372)G95 hbond (T0372)L62 1 SheetConstraint (T0372)F112 (T0372)D117 (T0372)N90 (T0372)G95 hbond (T0372)D117 1 SheetConstraint (T0372)E267 (T0372)Y261 (T0372)E236 (T0372)T230 hbond (T0372)Y261 1