CreatePredAlphaCost pred_alpha2k alpha11 T0296.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0296.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0296.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 20 backbone_clashes 2 \ break 50 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 20 \ 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 // 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: # known_ssbond 0.5 # 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. # include T0296.dssp-ehl2.constraints HelixConstraint I3 E15 0.8502 StrandConstraint T22 T24 0.632 HelixConstraint I37 E65 0.8489 StrandConstraint I70 S76 0.6285 HelixConstraint I80 G84 0.6857 HelixConstraint T90 E105 0.7575 StrandConstraint F110 I111 0.6007 HelixConstraint E127 A138 0.615 StrandConstraint V143 N148 0.7665 HelixConstraint M158 A172 0.6309 StrandConstraint L182 F185 0.6712 StrandConstraint V207 V211 0.6494 HelixConstraint V218 K225 0.787 HelixConstraint F231 R259 0.6466 StrandConstraint G265 D268 0.745 HelixConstraint V281 E287 0.8916 HelixConstraint G297 A316 0.6164 HelixConstraint E334 Q341 0.9182 HelixConstraint L347 T354 0.6131 StrandConstraint I364 A365 0.6056 HelixConstraint A372 I388 0.7444 StrandConstraint T393 I398 0.6324 StrandConstraint M406 E408 0.6654 StrandConstraint V418 K420 0.7806 HelixConstraint V427 S431 0.653 # the final sheet SheetConstraint L28 T24 T392 R396 hbond M25 1.0 # SheetConstraint (T0296)G265 (T0296)L269 (T0296)T415 (T0296)M419 hbond (T0296)L269 1 # SheetConstraint (T0296)G265 (T0296)L269 (T0296)T415 (T0296)M419 hbond (T0296)L269 1 include rr.constraints