CreatePredAlphaCost pred_alpha2k alpha11 T0347.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0347.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0347.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 30 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 50 backbone_clashes 2 \ break 200 \ pred_alpha2k 2 \ 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 \ 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. Constraint F5.CB D78.CB -10. 6.2 10.0 1 Constraint I34.CB K2.CB -10. 5.0 10.0 1 Constraint R12.CB F70.CB -10. 5.0 10.0 1 Constraint N13.CB W67.CB -10. 5.0 10.0 1 Constraint Q26.CB A52.CB -10. 8.0 10.0 1 Constraint D39.CB S83.CB -10. 7.2 10.0 1 Constraint L49.CB L94.CB -10. 5.0 10.0 1 Constraint A52.CB R98.CB -10. 6.7 10.0 1 Constraint Y55.CB R101.CB -10. 7.7 10.0 1 Constraint P61.CB H102.CB -10. 5.0 10.0 1 Constraint F65.CB E99.CB -10. 5.0 10.0 1 Constraint A68.CB K96.CB -10. 5.0 10.0 1