CreatePredAlphaCost pred_alpha2k alpha11 T0335.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0335.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0335.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 3 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 10 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ missing_atoms 1 # From the str2 alphabet HelixConstraint S3 G20 5 HelixConstraint T23 L49 5 HelixConstraint P64 N74 5 # Add hbond constraints from sep alphabets Hbond G59.N D56.O 10 Hbond D56.N N60.O 10 Hbond I54.O V62.N 10 Hbond L76.N Q71.O 10 Hbond K75.N R72.O 10 # Sheet constraint from the sep and notor alphabets. SheetConstraint I54 D56 V62 N60 hbond I54 20