CreatePredAlphaCost pred_alpha2k alpha11 T0334.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0334.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0334.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 7 \ n_ca_c 10 bad_peptide 10 \ bystroff 5 \ soft_clashes 80 backbone_clashes 2 \ break 240 \ 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 \ maybe_ssbond 0 // 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 T0334.dssp-ehl2.constraints //include T0334.undertaker-align.sheets //include rr.constraints HelixConstraint (T0334)G14 (T0334)L28 1 HelixConstraint (T0334)F59 (T0334)G64 1 HelixConstraint (T0334)P66 (T0334)M71 1 HelixConstraint (T0334)L122 (T0334)S130 1 HelixConstraint (T0334)P138 (T0334)Y144 1 HelixConstraint (T0334)P147 (T0334)A152 1 HelixConstraint (T0334)D172 (T0334)K187 1 HelixConstraint (T0334)T304 (T0334)H317 1 HelixConstraint (T0334)T359 (T0334)H374 1 HelixConstraint (T0334)P382 (T0334)A405 1 HelixConstraint (T0334)Q404 (T0334)F409 1 HelixConstraint (T0334)T415 (T0334)N421 1 HelixConstraint (T0334)A427 (T0334)G440 1 HelixConstraint (T0334)N457 (T0334)F462 1 HelixConstraint (T0334)N468 (T0334)L475 1 HelixConstraint (T0334)V474 (T0334)G479 1 HelixConstraint (T0334)M492 (T0334)E501 1 HelixConstraint (T0334)K507 (T0334)T516 1 HelixConstraint (T0334)S519 (T0334)R530 1 SheetConstraint (T0334)D6 (T0334)G12 (T0334)A32 (T0334)Q38 hbond (T0334)I8 1 SheetConstraint (T0334)K7 (T0334)G12 (T0334)D222 (T0334)C227 hbond (T0334)L9 1 SheetConstraint (T0334)T35 (T0334)A39 (T0334)R191 (T0334)D195 hbond (T0334)L36 1 SheetConstraint (T0334)A76 (T0334)Y78 (T0334)F171 (T0334)W169 hbond (T0334)S77 0.2 SheetConstraint (T0334)I82 (T0334)I85 (T0334)T273 (T0334)I276 hbond (T0334)K83 0.5 SheetConstraint (T0334)V80 (T0334)I85 (T0334)F111 (T0334)H106 hbond (T0334)F84 1 SheetConstraint (T0334)Y116 (T0334)H117 (T0334)P121 (T0334)I120 hbond (T0334)H117 1 SheetConstraint (T0334)E198 (T0334)R202 (T0334)T213 (T0334)E209 hbond (T0334)H199 1 SheetConstraint (T0334)S210 (T0334)T213 (T0334)D220 (T0334)R217 hbond (T0334)V211 1 SheetConstraint (T0334)F224 (T0334)D226 (T0334)C343 (T0334)S345 hbond (T0334)F224 1 SheetConstraint (T0334)P242 (T0334)M246 (T0334)R336 (T0334)V332 hbond (T0334)L244 1 SheetConstraint (T0334)A255 (T0334)P261 (T0334)V297 (T0334)R291 hbond (T0334)V256 1 SheetConstraint (T0334)D253 (T0334)A257 (T0334)F330 (T0334)N326 hbond (T0334)A257 1 SheetConstraint (T0334)T273 (T0334)M278 (T0334)I286 (T0334)G281 hbond (T0334)S274 1 SheetConstraint (T0334)S280 (T0334)M288 (T0334)S299 (T0334)R291 hbond (T0334)W282 1 SheetConstraint (T0334)G333 (T0334)N335 (T0334)F352 (T0334)S350 hbond (T0334)G333 1 SheetConstraint (T0334)A338 (T0334)V340 (T0334)S345 (T0334)C343 hbond (T0334)V340 1