CreatePredAlphaCost pred_alpha2k alpha11 T0289.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0289.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0289.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 25 near_backbone 15 way_back 5 dry5 25 dry6.5 30 dry8 25 dry12 5 \ phobic_fit 2 \ sidechain 10 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 40 backbone_clashes 2 \ break 80 \ 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 \ 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 T0289.dssp-ehl2.constraints # include T0289.undertaker-align.sheets # include rr.constraints # From T0289.dssp-ehl2.constraints StrandConstraint K12 G17 0.6734 HelixConstraint G26 K35 0.7282 StrandConstraint E46 F50 0.6427 HelixConstraint P54 T61 0.6369 HelixConstraint L74 N76 0.6065 HelixConstraint P86 F99 0.6801 StrandConstraint D109 D113 0.6332 StrandConstraint T124 I126 0.6071 HelixConstraint F134 C145 0.6388 HelixConstraint T166 S168 0.6026 StrandConstraint V174 V178 0.6754 HelixConstraint A188 I205 0.6002 # New constraints from notor alphabets: HelixConstraint N283 T297 0.679 Hbond H255.O D258.N 0.800 # From the undertaker-align.sheets #SheetConstraint (T0289)K11 (T0289)G17 (T0289)Y108 (T0289)L114 hbond (T0289)K12 41.5751 #SheetConstraint (T0289)K11 (T0289)G18 (T0289)L45 (T0289)T52 hbond (T0289)I13 41.5751 #SheetConstraint (T0289)D109 (T0289)N116 (T0289)K171 (T0289)V178 hbond (T0289)V111 41.5751 #SheetConstraint (T0289)N116 (T0289)T117 (T0289)G179 (T0289)P180 hbond (T0289)T117 41.5751 #SheetConstraint (T0289)C123 (T0289)L127 (T0289)V178 (T0289)V174 hbond (T0289)T124 41.5751 #SheetConstraint (T0289)T124 (T0289)L127 (T0289)P150 (T0289)V153 hbond (T0289)L125 41.5751 #SheetConstraint (T0289)L149 (T0289)V153 (T0289)I219 (T0289)K223 hbond (T0289)C151 41.5751 # New constraints: #SheetConstraint (T0289)P259 (T0289)S261 (T0289)L271 (T0289)K269 hbond (T0289)V260 20