// Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/ ReadTrainingAtoms monomeric-50pc.atoms ReadRotamerLibrary monomeric-50pc.rot InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/ ReadAtomType pdb-name.types ReadClashTable pdb-atom-name.clash SetClashDefinition pdb-atom-name CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist CreateAlphaCost alpha monomeric-smoothed-alpha.hist CreateAlphaCost alpha_prev monomeric-smoothed-alpha-1.hist -1 Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix ReadTargetPDB T0151.blank.pdb NameTarget T0151 PopConform // get rid of uneeded all-zero conformation InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix CreatePredAlphaCost pred_alpha2 alpha11 T0151.t2k.alpha.rdb 2 alpha alpha_prev // fix length of hairpin 1 Constraint 191 320 30 42.315 60 // CA A29 CA T44 // fix length of hairpin 2 Constraint 616 707 20 27.243 40 // CA R82 CA E92 // fix hairpin separation Constraint 320 707 30 43.683 70 // CA T44 CA E92 // fix spacing from hairpin2 to short hairpin Constraint 171 707 20 25.946 40 // CA S24 CA E92 // antiflop constraints: Constraint 340 771 20 29.382 40 // CA W47 E100 Constraint 408 707 15 25 40 // CA L55 E92 // Still more scaffolding constraints Constraint 118 272 20 32.970 40 // CA E18 I39 Constraint 389 652 10 19.239 30 // CA L53 R86 // interestingly the first antiparallel pair seems to have the same // center (44) as the second pair (hairpin1) Constraint 26 631 2 2.7 3.2 // N T5 O L83 Constraint 31 625 2 2.7 3.2 // O T5 N L83 Constraint 40 612 2 2.7 3.2 // N I7 O G81 Constraint 46 610 2 2.7 3.2 // O I7 N G81 Constraint 55 602 2 2.7 3.2 // N I9 O V79 Constraint 61 597 2 2.7 3.2 // O I9 N V79 Constraint 70 587 2 2.7 3.2 // N G11 O V77 Constraint 72 582 2 2.7 3.2 // O G11 N V77 Constraint 82 569 2 2.7 3.2 // N L13 O A75 Constraint 88 566 2 2.7 3.2 // O L13 N A75 // put in some hydrogen bonds for hairpin1 // A29-I59 S35-L53 I39-D49 Constraint 197 446 2 2.7 3.2 // N A29 O I59 Constraint 200 440 2 2.7 3.2 // O A29 N I59 Constraint 228 413 2 2.7 3.2 // N V33 O L55 Constraint 233 407 2 2.7 3.2 // O V33 N L55 Constraint 240 394 2 2.7 3.2 // N S35 O L53 Constraint 244 388 2 2.7 3.2 // O S35 N L53 Constraint 253 381 2 2.7 3.2 // N P37 O D51 Constraint 258 374 2 2.7 3.2 // O P37 N D51 Constraint 271 368 2 2.7 3.2 // N I39 O D49 Constraint 277 362 2 2.7 3.2 // O I39 N D49 // put in some CB spacing for hairpin 2, but make it weak, since the // register is not clear // FROM try1, it looks like x+y=184 for x<=80 // x+y=183 for x>=80 works Constraint 591 821 3 5.12 12 // CBs I78 I106 Constraint 606 804 3 5.12 12 // CBs S80 D104 // bulge near V103 Constraint 616 781 3 5.12 12 // CBs R82 v101 Constraint 635 764 3 5.12 12 // CBs K84 I99 Constraint 653 750 3 5.12 12 // CBs R86 T97 Constraint 670 730 3 5.12 12 // CBs F88 K95 Constraint 689 716 3 5.12 12 // CAs T90 G93 //try1 constraints // Constraint 653 739 3 5.12 12 // CBs R86 R96 // Constraint 670 730 3 5.12 12 // CBs F88 K95 // Constraint 690 721 3 5.12 12 // CBs T90 E94 // Old Hbonds, from when I was more confident about the register. // (before try1 in 1-111/) // Constraint 604 808 2 2.7 3.2 // N S80 O D104 // Constraint 608 802 2 2.7 3.2 // O S80 N D104 // Constraint 651 746 2 2.7 3.2 // N R86 O R96 // Constraint 660 737 2 2.7 3.2 // O R86 N R96 // Constraint 688 726 2 2.7 3.2 // N T90 O E94 // Constraint 693 719 2 2.7 3.2 // O T90 N E94 // put in some hydrogen bonds for short hairpin // R20-V28 Constraint 134 195 2 2.7 3.2 // N R20 O V28 Constraint 143 190 2 2.7 3.2 // O R20 N V28 // hold barrel together: Constraint 424 770 2 2.7 3.2 // O R56 N D100 Constraint 74 238 2 2.7 3.2 // N N12 O A34 SetCost gen6.5 0.2 wet6.5 0.2 dry5 1.0 dry6.5 2.0 dry8 1.0 dry12 1 \ phobic_fit 0.1 \ sidechain 0.2 \ clashes 1 sidechain_clashes -0.2 backbone_clashes 0.5 \ break 9 \ constraints 0.02 \ pred_alpha2 0.9 \ contact_order 1 // known_ssbond 0.5 // radius_norm 0 radius_fit 0.2 \