CreatePredAlphaCost pred_alpha2k alpha11 T0375.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0375.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0375.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 40 dry8 20 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 40 backbone_clashes 2 \ break 100 \ 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 // 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 T0375.dssp-ehl2.constraints # include T0375.undertaker-align.sheets # include rr.constraints # from try5 try6 # dry5 15 20 same # dry6.5 20 40 same # dry8 15 20 same # soft_clashes 20 40 same # break 50 100 200 # constraints 10 50 same HelixConstraint (T0375)A120 (T0375)T129 1 HelixConstraint (T0375)V168 (T0375)G182 1