CreatePredAlphaCost pred_alpha2k alpha11 XXX0000.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 XXX0000.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 XXX0000.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 25 dry8 20 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 50 backbone_clashes 2 \ break 75 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 10 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 60 \ hbond_geom_beta_pair 110 \ missing_atoms 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 T0370.dssp-ehl2.constraints //include T0370.undertaker-align.sheets //include rr.constraints KnownBreak M155 Constraint A31.CB A185.CB -10 5.5 6.0 0.5 Constraint W27.CB W181.CB -10 4.3 4.8 0.5 Constraint P38.CB P192.CB -10 6.3 6.8 0.5 Constraint A37.CB A191.CB -10 12.1 12.6 0.5 Constraint L82.CB L236.CB -10 18.4 6.2 0.5