CreatePredAlphaCost pred_alpha2k alpha11 T0319.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0319.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0319.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 15 \ 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 T0319.dssp-ehl2.constraints # I've increased the length and weight of the first strand StrandConstraint 2 9 1.6389 StrandConstraint P24 Q26 0.6902 HelixConstraint P44 V51 0.6191 HelixConstraint W56 E65 0.8578 HelixConstraint M90 Q102 0.6522 StrandConstraint E109 K111 0.6765 StrandConstraint I118 Y120 0.6486 HelixConstraint P132 H133 0.6016 # include T0319.undertaker-align.sheets include rr.0.2.constraints #try1 sheets SheetConstraint (T0319)A106 (T0319)R113 (T0319)N123 (T0319)G116 hbond (T0319)G108 5 # This next one looks rather small. Let's take it out for now # SheetConstraint (T0319)M110 (T0319)C112 (T0319)I82 (T0319)E84 hbond (T0319)K111 1 # I shifted this one slightly to tighten up the hairpin. SheetConstraint (T0319)H117 (T0319)I121 (T0319)L130 (T0319)P126 hbond (T0319)I118 5