// 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 T0132.blank.pdb NameTarget T0132 PopConform // get rid of uneeded all-zero conformation InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix CreatePredAlphaCost pred_alpha2 alpha11 T0132.t2k.alpha.rdb 2 alpha alpha_prev // add constraints to tack on first short strand Constraint 75 119 2.0 2.7 3.2 // N R11 O V16 Constraint 84 114 2.0 2.7 3.2 // O R11 N V16 // add constraints to hold first strand onto sheet // I THINK THIS IS MISALIGNED: // Constraint 131 629 2 5.12 7 // CB L18 CB L86 // Constraint 139 623 2 5.12 7 // CB L19 CB C85 // Constraint 147 614 2 5.12 7 // CB R20 CB Q84 // add constraints for hbonds in the first strand Constraint 121 610 2.0 2.7 3.2 // L17 N G83 O Constraint 127 608 2.0 2.7 3.2 // L17 O G83 N Constraint 137 594 2.0 2.7 3.2 // L19 N C81 O Constraint 143 590 2.0 2.7 3.2 // L19 O C81 N // add constraints for strand ending at F122 Constraint 678 919 2.0 2.7 3.2 // I93 N F122 O Constraint 684 910 2.0 2.7 3.2 // I93 O F122 N Constraint 695 901 2.0 2.7 3.2 // I95 N F120 O Constraint 701 892 2.0 2.7 3.2 // I95 O F120 N Constraint 712 883 2.0 2.7 3.2 // V97 N A118 O Constraint 717 880 2.0 2.7 3.2 // V97 O A118 N Constraint 728 870 2.0 2.7 3.2 // V99 N T116 O Constraint 733 865 2.0 2.7 3.2 // V99 O T116 N Constraint 749 856 2.0 2.7 3.2 // V101 N C114 O Constraint 754 852 2.0 2.7 3.2 // V101 O C114 N Constraint 765 838 2.0 2.7 3.2 // K103 N R112 O // add constraints to keep edge strand close Constraint 459 909 2.0 2.7 3.2 // A63 N T121 O Constraint 462 903 2.0 2.7 3.2 // A63 O T121 N // remove constraints near the bulge // Constraint 480 890 2.0 2.7 3.2 // N S66 O V119 // Constraint 484 885 2.0 2.7 3.2 // O S66 N V119 // The next two constraints are buggy: // Constraint 494 870 2.0 2.7 3.2 // N68 N T116 O // Constraint 500 865 2.0 2.7 3.2 // N68 O T116 N Constraint 494 878 2.0 2.7 3.2 // N68 N D117 O Constraint 500 872 2.0 2.7 3.2 // N68 O D117 N Constraint 513 863 2.0 2.7 3.2 // N I70 O V115 Constraint 519 858 2.0 2.7 3.2 // O I70 N V115 // add constraint to keep helix straight Constraint 273 385 20 22.5 27 // CA W38 CA E53 // After jiggling got things tight (try23), I removed the helix // packing constraints since they may have been driving things in // the wrong direction. // add constraints to pack helices: // I'm having trouble deciding between the next two for I149 // Constraint 1129 335 0 3.1 5 // CD1 I149 CA M45 // Constraint 1129 355 0 3.1 5 // CD1 I149 CA I49 // Constraint 1077 376 0 3.1 5 // CD2 L142 CA K52 // Constraint 1108 351 0 4 8 // CD2 L146 CB A48 // I'm no longer happy with this one // Constraint 1146 336 0 4 8 // C E151 CG M45 // I'm no longer convinced this is right. // add constraints to make N-terminus be on "right" side of sheet // Constraint 10 309 -20 6.0 15.0 // CA S2 CA Q42 SetCost gen6.5 0.2 wet6.5 0.2 dry5 1.0 dry6.5 1.0 dry8 1.0 dry12 1 \ radius_norm 0 radius_fit 0.2 \ sidechain 0.2 \ clashes 2 sidechain_clashes -0.2 backbone_clashes 0.5 \ break 7 \ constraints 0.05 \ pred_alpha2 1 \ contact_order 1 // known_ssbond 0.5 // alpha 1 alpha_prev 1 \