CreatePredAlphaCost pred_alpha2k alpha11 T0318.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0318.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0318.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. include rr.constraints # taken from T0318.t2k.str2.constraints StrandConstraint Q3 V6 2 StrandConstraint L20 V23 2 HelixConstraint T47 I56 2 StrandConstraint H73 T76 2 HelixConstraint N89 L97 2 StrandConstraint N108 A115 2 HelixConstraint L121 T130 2 StrandConstraint V150 K154 2 HelixConstraint T164 A174 2 SheetConstraint (T0318)L20 (T0318)V23 (T0318)V6 (T0318)Q3 hbond (T0318)L20 3 SheetConstraint (T0318)S19 (T0318)K25 (T0318)A72 (T0318)P78 hbond (T0318)I21 3 SheetConstraint (T0318)H73 (T0318)D79 (T0318)H110 (T0318)E116 hbond (T0318)L74 3 SheetConstraint (T0318)V109 (T0318)F111 (T0318)G140 (T0318)R142 hbond (T0318)F111 3 SheetConstraint (T0318)L113 (T0318)Y117 (T0318)V150 (T0318)K154 hbond (T0318)A115 3