CreatePredAlphaCost pred_alpha2k alpha11 T0348.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0348.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0348.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 25 dry8 20 dry12 5 \ phobic_fit 5 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 60 backbone_clashes 2 \ break 100 \ 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 4 \ 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 T0348.dssp-ehl2.constraints //include T0348.undertaker-align.sheets //include rr.constraints SheetConstraint (T0348)L18 (T0348)K22 (T0348)C29 (T0348)D25 hbond (T0348)V19 1 SheetConstraint (T0348)D25 (T0348)C29 (T0348)I38 (T0348)L34 hbond (T0348)L27 1 SheetConstraint (T0348)I38 (T0348)K39 (T0348)P43 (T0348)I42 hbond (T0348)K39 1 Constraint D32.OD1 C11.CB -10. 7.0 14.0 4 Constraint C14.CB C29.CB -10. 7.0 14.0 2 HelixConstraint (T0348)A3 (T0348)V10 2 HelixConstraint (T0348)P43 (T0348)L53 2 HelixConstraint (T0348)A54 (T0348)H68 2