CreatePredAlphaCost pred_alpha2k alpha11 T0358.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0358.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0358.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 25 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 70 backbone_clashes 2 \ break 150 \ 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 \ maybe_ssbond 0 // 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 T0358.dssp-ehl2.constraints //include T0358.undertaker-align.sheets //include rr.constraints //from try21-opt2.helices HelixConstraint (T0358)M1 (T0358)T21 4 HelixConstraint (T0358)A59 (T0358)G71 2 HelixConstraint (T0358)D75 (T0358)H87 2 //from try21-opt2.sheets SheetConstraint (T0358)Y24 (T0358)S25 (T0358)D43 (T0358)R42 hbond (T0358)S25 2 SheetConstraint (T0358)I27 (T0358)E30 (T0358)V41 (T0358)R38 hbond (T0358)T28 2 SheetConstraint (T0358)L39 (T0358)D43 (T0358)R51 (T0358)R47 hbond (T0358)L39 2 SheetConstraint (T0358)V49 (T0358)A52 (T0358)A59 (T0358)E56 hbond (T0358)W50 2