CreatePredAlphaCost pred_alpha2k alpha11 T0356.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0356.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0356.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 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 T0356.dssp-ehl2.constraints //include T0356.undertaker-align.sheets //include rr.constraints # from M1-A180/try6-opt2.helices and sheets HelixConstraint (T0356)M1 (T0356)G20 20 HelixConstraint (T0356)P31 (T0356)A45 20 HelixConstraint (T0356)F67 (T0356)G78 20 HelixConstraint (T0356)E80 (T0356)K90 20 HelixConstraint (T0356)G89 (T0356)E97 20 HelixConstraint (T0356)F104 (T0356)L111 20 HelixConstraint (T0356)D109 (T0356)N119 20 HelixConstraint (T0356)P121 (T0356)R126 20 HelixConstraint (T0356)A128 (T0356)D138 20 HelixConstraint (T0356)I145 (T0356)W151 20 HelixConstraint (T0356)W151 (T0356)A156 20 HelixConstraint (T0356)D154 (T0356)W161 20 SheetConstraint (T0356)A49 (T0356)N54 (T0356)L63 (T0356)Y58 hbond (T0356)L50 50 SheetConstraint (T0356)F52 (T0356)N54 (T0356)I25 (T0356)L27 hbond (T0356)E53 50 SheetConstraint (T0356)G162 (T0356)P169 (T0356)Y179 (T0356)E172 hbond (T0356)T164 50 #From T140-F340 try8-opt2.helices and .sheets. SheetConstraint (T0356)T160 (T0356)H170 (T0356)L183 (T0356)R173 hbond (T0356)T160 50 SheetConstraint (T0356)R180 (T0356)I184 (T0356)M191 (T0356)N187 hbond (T0356)Q182 50 SheetConstraint (T0356)L189 (T0356)R192 (T0356)V217 (T0356)A220 hbond (T0356)I190 50 SheetConstraint (T0356)G250 (T0356)V255 (T0356)L263 (T0356)C258 hbond (T0356)T251 50 SheetConstraint (T0356)V272 (T0356)Y276 (T0356)H308 (T0356)F304 hbond (T0356)L273 50 SheetConstraint (T0356)F304 (T0356)I309 (T0356)G323 (T0356)H318 hbond (T0356)F304 50 HelixConstraint (T0356)G199 (T0356)H210 20 HelixConstraint (T0356)P225 (T0356)T233 20 HelixConstraint (T0356)T233 (T0356)T238 20 HelixConstraint (T0356)S240 (T0356)L248 20 HelixConstraint (T0356)D327 (T0356)F340 20 # From T320-S496 try3-opt2.sheets and .helices SheetConstraint (T0356)E350 (T0356)L356 (T0356)I370 (T0356)R364 hbond (T0356)E350 50 SheetConstraint (T0356)Y363 (T0356)V367 (T0356)A424 (T0356)V428 hbond (T0356)L365 50 SheetConstraint (T0356)F397 (T0356)D402 (T0356)R425 (T0356)V430 hbond (T0356)I399 50 SheetConstraint (T0356)V398 (T0356)D403 (T0356)G448 (T0356)L453 hbond (T0356)V400 50 SheetConstraint (T0356)D402 (T0356)D403 (T0356)E431 (T0356)N432 hbond (T0356)D403 50 HelixConstraint (T0356)P326 (T0356)V339 20 HelixConstraint (T0356)V339 (T0356)F348 20 HelixConstraint (T0356)Y374 (T0356)Q391 20 HelixConstraint (T0356)R408 (T0356)D422 20 HelixConstraint (T0356)P434 (T0356)S442 20 HelixConstraint (T0356)F440 (T0356)S445 20 HelixConstraint (T0356)D474 (T0356)L488 20 HelixConstraint (T0356)D486 (T0356)N493 20