CreatePredAlphaCost pred_alpha2k alpha11 T0320.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0320.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0320.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 100 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 50 \ 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. #taking sheet constraints from try1-opt2.helices HelixConstraint S4 Y11 1 HelixConstraint I13 L18 1 HelixConstraint Q25 Q31 1 HelixConstraint T30 K39 1 HelixConstraint C66 S75 1 HelixConstraint D91 F97 1 HelixConstraint Q95 Q100 1 HelixConstraint F113 Y127 1 HelixConstraint M144 I154 1 HelixConstraint D198 S209 1 #taking sheet constraints from try1-opt2.sheets SheetConstraint I56 F58 A160 V162 hbond S57 1 SheetConstraint S57 S59 P103 V105 hbond F58 1 SheetConstraint T104 D108 L131 Q135 hbond T104 1 SheetConstraint E159 I163 F188 Q192 hbond I161 1 SheetConstraint I178 D182 Q192 F188 hbond R180 1 SheetConstraint F280 Y283 L293 G290 hbond S281 1 #adding constraints from the second domain runs, from try8: HelixConstraint D258 K277 1.0 HelixConstraint L216 P232 0.6 StrandConstraint L245 F255 1.0 HelixConstraint T297 R300 0.6498 StrandConstraint Y288 V294 1.0 include rr.constraints