CreatePredAlphaCost pred_alpha2k alpha11 T0379.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0379.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0379.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 7 \ phobic_fit 2 \ sidechain 4 \ 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 9 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ 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 T0379.dssp-ehl2.constraints include T0379.undertaker-align.sheets include rr.constraints //included to help with burial Constraint F153.CB T179.CB -10. 7.0 14.0 0.5 Constraint F169.CB A180.CB -10. 7.0 14.0 0.5