CreatePredAlphaCost pred_alpha2k alpha11 T0320.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0320.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0320.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 100 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 50 \ 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 T0320.dssp-ehl2.constraints #I am removing the constraints from the subdomain: HelixConstraint I20 S50 0.6087 StrandConstraint I56 Y60 0.7243 HelixConstraint D65 C76 0.6051 StrandConstraint I83 Q86 0.7473 HelixConstraint P98 V105 0.6576 HelixConstraint E117 R126 0.6078 HelixConstraint D150 K153 0.7326 StrandConstraint A160 G164 0.6599 StrandConstraint M189 L191 0.6012 HelixConstraint L199 Y208 0.8507 #HelixConstraint F247 A254 0.6228 #HelixConstraint V274 S281 0.6414 #StrandConstraint W291 L293 0.7134 #HelixConstraint L298 A301 0.6988 #and instead adding our own constraints from try8 in the subdomain runs: HelixConstraint D258 K277 1.0 HelixConstraint L216 P232 0.6 StrandConstraint L245 F255 1.0 HelixConstraint T297 R300 0.6498 StrandConstraint Y288 V294 1.0 #include T0320.undertaker-align.sheets #I am commenting out the sheet constraints for the subdomain except 280-282/291-293: #sheet constraints from conformation 0 T0320-1sur-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1sur SheetConstraint (T0320)I56 (T0320)F58 (T0320)A160 (T0320)V162 hbond (T0320)S57 52.5144 SheetConstraint (T0320)S57 (T0320)S59 (T0320)E79 (T0320)F81 hbond (T0320)F58 52.5144 SheetConstraint (T0320)E79 (T0320)K84 (T0320)D108 (T0320)F113 hbond (T0320)Y80 52.5144 SheetConstraint (T0320)E159 (T0320)V162 (T0320)F188 (T0320)L191 hbond (T0320)I161 52.5144 SheetConstraint (T0320)I178 (T0320)S183 (T0320)Q192 (T0320)D187 hbond (T0320)R180 52.5144 #sheet constraints from conformation 1 T0320-1gpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1gpmA SheetConstraint (T0320)I56 (T0320)F58 (T0320)A160 (T0320)V162 hbond (T0320)S57 36.4717 SheetConstraint (T0320)S57 (T0320)Y60 (T0320)P103 (T0320)F106 hbond (T0320)F58 36.4717 SheetConstraint (T0320)T104 (T0320)Q109 (T0320)L131 (T0320)R136 hbond (T0320)T104 36.4717 SheetConstraint (T0320)A160 (T0320)I163 (T0320)M189 (T0320)Q192 hbond (T0320)I161 36.4717 ##SheetConstraint (T0320)V275 (T0320)D276 (T0320)N228 (T0320)N229 hbond (T0320)D276 36.4717 SheetConstraint (T0320)F280 (T0320)K282 (T0320)L293 (T0320)W291 hbond (T0320)S281 36.4717 #sheet constraints from conformation 2 T0320-1wy5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1wy5A SheetConstraint (T0320)S57 (T0320)F58 (T0320)I161 (T0320)V162 hbond (T0320)S57 29.6818 SheetConstraint (T0320)S57 (T0320)Y60 (T0320)P103 (T0320)F106 hbond (T0320)F58 29.6818 SheetConstraint (T0320)I83 (T0320)K84 (T0320)G54 (T0320)E55 hbond (T0320)K84 29.6818 SheetConstraint (T0320)P103 (T0320)F106 (T0320)S130 (T0320)E133 hbond (T0320)T104 29.6818 SheetConstraint (T0320)A160 (T0320)I163 (T0320)M189 (T0320)Q192 hbond (T0320)I161 29.6818 ##SheetConstraint (T0320)S265 (T0320)T269 (T0320)V275 (T0320)P271 hbond (T0320)I267 29.6818 #sheet constraints from conformation 3 T0320-1xngA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1xngA SheetConstraint (T0320)E55 (T0320)F58 (T0320)T158 (T0320)I161 hbond (T0320)S57 22.3777 SheetConstraint (T0320)S57 (T0320)Y60 (T0320)P103 (T0320)F106 hbond (T0320)F58 22.3777 SheetConstraint (T0320)T104 (T0320)F106 (T0320)L131 (T0320)E133 hbond (T0320)T104 22.3777 #sheet constraints from conformation 4 T0320-1ni5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1ni5A SheetConstraint (T0320)E55 (T0320)F58 (T0320)E159 (T0320)V162 hbond (T0320)S57 16.5033 SheetConstraint (T0320)S57 (T0320)Y60 (T0320)P103 (T0320)F106 hbond (T0320)F58 16.5033 SheetConstraint (T0320)F82 (T0320)I83 (T0320)G54 (T0320)E55 hbond (T0320)I83 16.5033 SheetConstraint (T0320)T104 (T0320)D108 (T0320)L131 (T0320)Q135 hbond (T0320)T104 16.5033 SheetConstraint (T0320)I161 (T0320)V162 (T0320)R190 (T0320)L191 hbond (T0320)I161 16.5033 #sheet constraints from conformation 5 T0320-1wxiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1wxiA SheetConstraint (T0320)E55 (T0320)S59 (T0320)P103 (T0320)I107 hbond (T0320)I56 15.2659 SheetConstraint (T0320)E55 (T0320)S57 (T0320)A160 (T0320)V162 hbond (T0320)S57 15.2659 SheetConstraint (T0320)V105 (T0320)E110 (T0320)S130 (T0320)Q135 hbond (T0320)F106 15.2659 SheetConstraint (T0320)R190 (T0320)Q192 (T0320)V162 (T0320)G164 hbond (T0320)L191 15.2659 #sheet constraints from conformation 6 T0320-1vl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1vl2A SheetConstraint (T0320)S57 (T0320)Y60 (T0320)P103 (T0320)F106 hbond (T0320)F58 14.8449 SheetConstraint (T0320)P103 (T0320)D108 (T0320)S130 (T0320)Q135 hbond (T0320)T104 14.8449 #sheet constraints from conformation 7 T0320-1kqpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1kqpA SheetConstraint (T0320)S57 (T0320)S59 (T0320)V105 (T0320)I107 hbond (T0320)F58 13.9172 SheetConstraint (T0320)V105 (T0320)D108 (T0320)S130 (T0320)E133 hbond (T0320)F106 13.9172 #sheet constraints from conformation 8 T0320-1q15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1q15A SheetConstraint (T0320)H19 (T0320)I20 (T0320)Y208 (T0320)S209 hbond (T0320)I20 12.4396 SheetConstraint (T0320)I56 (T0320)F58 (T0320)A160 (T0320)V162 hbond (T0320)S57 12.4396 SheetConstraint (T0320)S57 (T0320)Y60 (T0320)P103 (T0320)F106 hbond (T0320)F58 12.4396 SheetConstraint (T0320)L102 (T0320)F106 (T0320)L129 (T0320)E133 hbond (T0320)T104 12.4396 SheetConstraint (T0320)D108 (T0320)Q109 (T0320)F113 (T0320)T112 hbond (T0320)Q109 12.4396 SheetConstraint (T0320)A160 (T0320)I163 (T0320)M189 (T0320)Q192 hbond (T0320)I161 12.4396 #sheet constraints from conformation 9 T0320-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:2d13A SheetConstraint (T0320)I56 (T0320)F58 (T0320)A160 (T0320)V162 hbond (T0320)S57 10.9989 SheetConstraint (T0320)T104 (T0320)F106 (T0320)F58 (T0320)Y60 hbond (T0320)V105 10.9989 SheetConstraint (T0320)T104 (T0320)D108 (T0320)L131 (T0320)Q135 hbond (T0320)F106 10.9989 SheetConstraint (T0320)A160 (T0320)I163 (T0320)M189 (T0320)Q192 hbond (T0320)I161 10.9989 ##SheetConstraint (T0320)I272 (T0320)V275 (T0320)L293 (T0320)G290 hbond (T0320)S273 10.9989 include rr.constraints