CreatePredAlphaCost pred_alpha2k alpha11 T0203.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0203.t04.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 8 dry12 8 \ phobic_fit 5 \ sidechain 6 \ bystroff 5 \ soft_clashes 20 backbone_clashes 2 \ break 80 \ pred_alpha04 6 \ pred_alpha2k 6 \ constraints 10 \ hbond_geom 0.1 \ hbond_geom_backbone 0.2 \ hbond_geom_beta 0.4 \ hbond_geom_beta_pair 1 // Add the following for extra-cellular proteins: # known_ssbond 0.5 # and add SSbond commands # maybe_ssbond 0.5 // For comparative modeling, increase weight of break and hbond_geom... // put any constraints here, such as helix constraints, strand constraints, // ssbond, hbond, or just arbitrary pairs of atoms. # grep -h HelixC *.constraints # and merge compatible predictions HelixConstraint W36 H38 1 HelixConstraint A40 K56 9 HelixConstraint P66 Q75 9 HelixConstraint W136 E150 9 HelixConstraint E178 L181 1 HelixConstraint K192 L203 9 HelixConstraint G223 C230 0.5 HelixConstraint Q249 I264 9 HelixConstraint E286 S289 2 HelixConstraint I330 T342 9 HelixConstraint A354 L359 9 # grep -h StrandC *.constraints # eliminate any that are only 2 long and merge compatible StrandConstraint Y13 P16 2 StrandConstraint T25 P30 9 StrandConstraint E58 S65 9 StrandConstraint I80 S86 6 StrandConstraint R81 M85 6 StrandConstraint T98 R102 9 StrandConstraint R104 V106 2 StrandConstraint I115 A124 9 StrandConstraint M159 E162 9 StrandConstraint S165 V168 9 StrandConstraint G172 T177 9 StrandConstraint S207 L211 9 StrandConstraint V236 T242 9 StrandConstraint R269 P281 2 StrandConstraint K270 L276 9 StrandConstraint Y283 T285 2 StrandConstraint S310 A317 9 StrandConstraint G320 A323 9 StrandConstraint H346 E352 9 StrandConstraint I364 T368 6 StrandConstraint Q370 P372 2 # file generated by validate2rr # based on 104 inputs. # limited to raw score .7 or greater # Constraint S90.CB A124.CB -10. 7.0 12.0 0.952 Constraint V237.CB I271.CB -10. 7.0 12.0 0.924 Constraint S90.CB W120.CB -10. 7.0 12.0 0.778 Constraint V236.CB I274.CB -10. 7.0 12.0 0.741 # constraints from the t04-thin35 # Constraint A40.CB D79.CB -10. 7.0 12.0 1.28003 # Constraint H11.CB V259.CB -10. 7.0 12.0 0.909871 # Constraint G12.CA F57.CB -10. 7.0 12.0 0.864246 # Constraint S90.CB A116.CB -10. 7.0 12.0 0.719616 # constraints from the t04-thin40 # Constraint P77.CB T246.CB -10. 7.0 12.0 0.858271 Constraint P77.CB K145.CB -10. 7.0 12.0 0.708367 Constraint N35.CB V46.CB -10. 7.0 12.0 0.701345 # constraints from the t04-thin62 # Constraint N35.CB T242.CB -10. 7.0 12.0 0.865302 Constraint T242.CB Q249.CB -10. 7.0 12.0 0.806991 # Constraint N35.CB S90.CB -10. 7.0 12.0 0.803925 # cluster conserved Constraint D169.OD2 H224.NE2 3.0 6.0 8.0 1 Constraint N187.CG H224.NE2 3.0 6.0 8.0 1 # cluster conserved Constraint D226.OD2 C366.SG 3.0 6.0 8.0 1 Constraint D226.OD2 N313.CG 3.0 6.0 8.0 1 Constraint N313.CG C366.SG 3.0 6.0 8.0 1 Constraint C229.SG C366.SG 3.0 8.0 12.0 1 Constraint C229.CG N313.CG 3.0 8.0 12.0 1 Constraint C230.SG C366.SG 3.0 8.0 12.0 1 Constraint C230.CG N313.CG 3.0 8.0 12.0 1 # from try18-opt2.sheets # These look mostly bogus! SheetConstraint A23 G28 V60 S65 hbond T25 5.0 # SheetConstraint N121 N129 N129 N121 hbond F122 SheetConstraint G126 A128 H157 M159 hbond G127 3.0 # SheetConstraint L182 K184 R213 L215 hbond L182 # SheetConstraint L211 L215 R252 P248 hbond R213 # SheetConstraint C229 A232 L239 V236 hbond C230 # SheetConstraint Q249 E251 A266 I264 hbond E251 # SheetConstraint L282 M284 G235 V237 hbond Y283 # SheetConstraint F314 A317 P324 I321 hbond Y315 #from try19-opt2.sheets # SheetConstraint I209 R213 E178 L182 hbond W210 # SheetConstraint M228 A232 S240 V236 hbond C230 # SheetConstraint A317 N318 I322 I321 hbond N318 #from try16-opt2.sheets # SheetConstraint Q24 W26 Q371 Q369 hbond W26 # back up 2 and lengthen SheetConstraint Q24 I27 Q369 C366 hbond W26 5.0 # SheetConstraint W120 A124 G131 G127 hbond F122 # find better pairing SheetConstraint R81 M85 S95 W91 hbond D94 5.0 SheetConstraint W91 S95 R102 T98 hbond S95 5.0 SheetConstraint T98 R102 D119 I115 hbond V101 1.0 # SheetConstraint G127 A128 H157 S158 hbond A128 # SheetConstraint I160 L161 N129 D130 hbond I160 # SheetConstraint G131 C132 D169 V168 hbond C132 # still questionable, but possible # SheetConstraint G127 G131 M159 G163 hbond A128 2.0 # I don't really like E178-N183 as a strand, but I don't see much choice # SheetConstraint G172 V176 N183 E179 hbond C174 1.0 # SheetConstraint E178 N183 I209 G214 hbond L182 1.0 # I don't believe these # SheetConstraint L211 Y216 R252 D247 hbond R213 # SheetConstraint M228 A232 S240 V236 hbond C230 # SheetConstraint G235 L238 L282 T285 hbond V237 SheetConstraint V236 W241 L276 I271 hbond V237 4.0 # lengthened SheetConstraint V312 A317 F326 I321 hbond Y315 3.0 # added SheetConstraint G320 A223 V348 I351 hbond V348 3.0