CreatePredAlphaCost pred_alpha2k alpha11 T0355.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0355.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0355.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 35 dry8 30 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 40 backbone_clashes 2 \ break 120 \ pred_alpha2k 4 \ pred_alpha04 .2 \ pred_alpha06 .2 \ constraints 15 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 70 \ hbond_geom_beta_pair 140 \ missing_atoms 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 T0355.dssp-ehl2.constraints include T0355.t2k.dssp-ehl2.constraints //include T0355.undertaker-align.sheets //include rr.constraints # these next two look good SheetConstraint (T0355)L22 (T0355)C28 (T0355)H62 (T0355)N68 hbond (T0355)G24 1 # we shift 102-106 up 2 SheetConstraint (T0355)G63 (T0355)E67 (T0355)G104 (T0355)L108 hbond (T0355)L64 20 # we shift 104-106 up 2 SheetConstraint (T0355)N106 (T0355)N110 (T0355)F126 (T0355)N130 hbond (T0355)V107 20 # we shift 161-164 up 2 SheetConstraint (T0355)F126 (T0355)V129 (T0355)K163 (T0355)A166 hbond (T0355)I127 20 # we shift 163-168 up 2 SheetConstraint (T0355)F165 (T0355)V170 (T0355)G197 (T0355)G202 hbond (T0355)A166 20 SheetConstraint (T0355)G197 (T0355)T201 (T0355)P224 (T0355)G228 hbond (T0355)V198 1 SheetConstraint (T0355)L225 (T0355)G228 (T0355)S244 (T0355)I247 hbond (T0355)V227 1 SheetConstraint (T0355)K20 (T0355)M25 (T0355)S244 (T0355)A249 hbond (T0355)A21 1