CreatePredAlphaCost pred_alpha2k alpha11 T0360.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0360.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0360.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 25 dry8 20 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 1.5 \ 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 T0360.dssp-ehl2.constraints //include T0360.undertaker-align.sheets //include rr.constraints //from try1-opt2.helices HelixConstraint (T0360)M1 (T0360)M18 1 HelixConstraint (T0360)T17 (T0360)I31 1 HelixConstraint (T0360)I48 (T0360)L56 1 HelixConstraint (T0360)D60 (T0360)R66 1 HelixConstraint (T0360)V67 (T0360)R73 1 HelixConstraint (T0360)R74 (T0360)L81 1 //from try2-opt2.helices HelixConstraint (T0360)T99 (T0360)H109 1 HelixConstraint (T0360)Q107 (T0360)Q114 1 HelixConstraint (T0360)V112 (T0360)E141 1 SheetConstraint (T0360)Y35 (T0360)V37 (T0360)K42 (T0360)R40 hbond (T0360)V37 1 SheetConstraint (T0360)R87 (T0360)D89 (T0360)A45 (T0360)P43 hbond (T0360)A45 4