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 40 backbone_clashes 4 \ break 90 \ pred_alpha04 12 \ pred_alpha2k 12 \ constraints 5 \ hbond_geom 0.1 \ hbond_geom_backbone 0.2 \ hbond_geom_beta 0.4 \ hbond_geom_beta_pair 0.8 // 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 0.2 StrandConstraint T25 P30 1.0 StrandConstraint E58 S65 1.0 StrandConstraint I80 S86 0.6 StrandConstraint R81 M85 0.6 StrandConstraint T98 R102 1.0 StrandConstraint R104 V106 0.2 StrandConstraint I115 A124 1.0 StrandConstraint M159 E162 1.0 StrandConstraint S165 V168 1.0 StrandConstraint G172 T177 1.0 StrandConstraint S207 L211 1.0 StrandConstraint V236 T242 1.0 StrandConstraint R269 P281 0.2 StrandConstraint K270 L276 1.0 StrandConstraint Y283 T285 0.2 StrandConstraint S310 A317 1.0 StrandConstraint G320 A323 1.0 StrandConstraint H346 E352 1.0 StrandConstraint I364 T368 0.6 StrandConstraint Q370 P372 0.2 # 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 5.0 8.0 0.5 Constraint D226.OD2 N313.CG 3.0 5.0 8.0 0.5 Constraint N313.CG C366.SG 3.0 5.0 8.0 0.5 Constraint C229.SG C366.SG 3.0 7.0 12.0 0.5 Constraint C229.CG N313.CG 3.0 7.0 12.0 0.5 Constraint C230.SG C366.SG 3.0 7.0 12.0 0.5 Constraint C230.CG N313.CG 3.0 7.0 12.0 0.5 # from try18-opt2.sheets # These look mostly bogus! SheetConstraint A23 G28 V60 S65 hbond T25 10 # SheetConstraint N121 N129 N129 N121 hbond F122 SheetConstraint G126 A128 H157 M159 hbond G127 10 # 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 10 # SheetConstraint W120 A124 G131 G127 hbond F122 # find better pairing SheetConstraint R81 M85 S95 W91 hbond D94 10 SheetConstraint W91 S95 R102 T98 hbond S95 10 SheetConstraint T98 R102 D119 I115 hbond V101 10 # 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 60 # 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 10 # lengthened SheetConstraint V312 A317 F326 I321 hbond Y315 10 # added SheetConstraint G320 A223 V348 I351 hbond V348 10