CreatePredAlphaCost pred_alpha2k alpha11 T0354.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0354.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0354.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 30 \ 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. #using try7's sheet's: SheetConstraint (T0354)D21 (T0354)L30 (T0354)G42 (T0354)L33 hbond (T0354)I22 1 SheetConstraint (T0354)V39 (T0354)D43 (T0354)G68 (T0354)H72 hbond (T0354)A40 1 SheetConstraint (T0354)L79 (T0354)A82 (T0354)H88 (T0354)V85 hbond (T0354)V80 1 #try7's helices HelixConstraint (T0354)M1 (T0354)K18 1 HelixConstraint (T0354)N45 (T0354)A62 1 HelixConstraint (T0354)V94 (T0354)D99 1 HelixConstraint (T0354)I100 (T0354)G106 1 HelixConstraint (T0354)P118 (T0354)H130 1 #adding a sheet constraint to keep the Proteinshopped model in place SheetConstraint (T0354)V67 (T0354)G71 (T0354)L79 (T0354)G83 hbond (T0354)S69 20