CreatePredAlphaCost pred_alpha2k alpha11 T0314.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0314.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0314.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 15 way_back 5 dry5 15 dry6.5 40 dry8 35 dry12 15 \ phobic_fit 10 \ sidechain 10 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 60 backbone_clashes 2 \ break 200 \ 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 0.5 \ 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 T0314.dssp-ehl2.constraints # include T0314.undertaker-align.sheets # include rr.constraints # from T0314.dssp-ehl2.constraints with higher weights: #HelixConstraint T6 A14 1 #HelixConstraint R63 E74 1 #StrandConstraint R27 F32 1 # New constraints: # StrandConstraint L88 R92 3 #SheetConstraint (T0314)R27 (T0314)F32 (T0314)R92 (T0314)L88 hbond (T0314)R27 3 # Take out all constraints and try to bury residues: #Constraint L72.CB I29.CB -10. 7.0 14.0 1 #Constraint L72.CB V41.CB -10. 7.0 14.0 1 #Constraint V41.CB I29.CB -10. 7.0 14.0 1