CreatePredAlphaCost pred_alpha2k alpha11 T0306.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0306.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0306.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 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. HelixConstraint (T0306)R64 (T0306)E70 SheetConstraint (T0306)M1 (T0306)T7 (T0306)H16 (T0306)I10 hbond (T0306)K2 1 SheetConstraint (T0306)K23 (T0306)D31 (T0306)A49 (T0306)A41 hbond (T0306)K23 1 SheetConstraint (T0306)W54 (T0306)S61 (T0306)C77 (T0306)E84 hbond (T0306)V55 1 SheetConstraint (T0306)I79 (T0306)E84 (T0306)V91 (T0306)V86 hbond (T0306)G80 1