SetSeed InfilePrefix // Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/ ReadTrainingAtoms dunbrack-2191.atoms ReadRotamerLibrary dunbrack-2191.rot InFilePrefix /projects/compbio/experiments/undertaker/spots/ ReadAtomType exp-pdb.types ReadClashTable exp-pdb-2191-2symm.clash SetClashDefinition exp-pdb-2191-2symm CreateBurialCost near_backbone near-backbone-center.spot smoothed-near-backbone-2spot.hist near-backbone-count.spot CreateBurialCost way_back way-back-center.spot smoothed-way-back-2spot.hist way-back-count.spot 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 dunbrack-2191-alpha.hist CreateAlphaCost alpha_prev dunbrack-2191-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 T0295.blank.pdb ReadTargetSeq T0295.a2m 1 NameTarget T0295 PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix include try2.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Switch to the following (commenting out the TryAllAlign) // to polish existing models InfilePrefix decoys/ ReadConformPDB T0295.try1-opt1-scwrl.pdb ReadConformPDB T0295.try1-opt1.pdb ReadConformPDB T0295.try1-opt2.gromacs0.pdb ReadConformPDB T0295.try1-opt2.pdb ReadConformPDB T0295.try1-opt2.repack-nonPC.pdb ReadConformPDB servers/3D-JIGSAW_POPULUS_TS1.pdb NameConform 3D-JIGSAW_POPULUS_TS1 SCWRLConform NameConform 3D-JIGSAW_POPULUS_TS1-scwrl ReadConformPDB servers/3D-JIGSAW_POPULUS_TS2.pdb NameConform 3D-JIGSAW_POPULUS_TS2 SCWRLConform NameConform 3D-JIGSAW_POPULUS_TS2-scwrl ReadConformPDB servers/3D-JIGSAW_POPULUS_TS3.pdb NameConform 3D-JIGSAW_POPULUS_TS3 SCWRLConform NameConform 3D-JIGSAW_POPULUS_TS3-scwrl ReadConformPDB servers/3D-JIGSAW_POPULUS_TS4.pdb NameConform 3D-JIGSAW_POPULUS_TS4 SCWRLConform NameConform 3D-JIGSAW_POPULUS_TS4-scwrl ReadConformPDB servers/3D-JIGSAW_POPULUS_TS5.pdb NameConform 3D-JIGSAW_POPULUS_TS5 SCWRLConform NameConform 3D-JIGSAW_POPULUS_TS5-scwrl ReadConformPDB servers/3D-JIGSAW_RECOM_TS1.pdb NameConform 3D-JIGSAW_RECOM_TS1 SCWRLConform NameConform 3D-JIGSAW_RECOM_TS1-scwrl ReadConformPDB servers/3D-JIGSAW_RECOM_TS2.pdb NameConform 3D-JIGSAW_RECOM_TS2 SCWRLConform NameConform 3D-JIGSAW_RECOM_TS2-scwrl ReadConformPDB servers/3D-JIGSAW_RECOM_TS3.pdb NameConform 3D-JIGSAW_RECOM_TS3 SCWRLConform NameConform 3D-JIGSAW_RECOM_TS3-scwrl ReadConformPDB servers/3D-JIGSAW_RECOM_TS4.pdb NameConform 3D-JIGSAW_RECOM_TS4 SCWRLConform NameConform 3D-JIGSAW_RECOM_TS4-scwrl ReadConformPDB servers/3D-JIGSAW_RECOM_TS5.pdb NameConform 3D-JIGSAW_RECOM_TS5 SCWRLConform NameConform 3D-JIGSAW_RECOM_TS5-scwrl ReadConformPDB servers/3D-JIGSAW_TS1.pdb NameConform 3D-JIGSAW_TS1 SCWRLConform NameConform 3D-JIGSAW_TS1-scwrl ReadConformPDB servers/3D-JIGSAW_TS2.pdb NameConform 3D-JIGSAW_TS2 SCWRLConform NameConform 3D-JIGSAW_TS2-scwrl ReadConformPDB servers/3Dpro_TS1.pdb NameConform 3Dpro_TS1 SCWRLConform NameConform 3Dpro_TS1-scwrl ReadConformPDB servers/3Dpro_TS2.pdb NameConform 3Dpro_TS2 SCWRLConform NameConform 3Dpro_TS2-scwrl ReadConformPDB servers/3Dpro_TS3.pdb NameConform 3Dpro_TS3 SCWRLConform NameConform 3Dpro_TS3-scwrl ReadConformPDB servers/3Dpro_TS4.pdb NameConform 3Dpro_TS4 SCWRLConform NameConform 3Dpro_TS4-scwrl ReadConformPDB servers/3Dpro_TS5.pdb NameConform 3Dpro_TS5 SCWRLConform NameConform 3Dpro_TS5-scwrl ReadConformPDB servers/ABIpro_TS1.pdb NameConform ABIpro_TS1 SCWRLConform NameConform ABIpro_TS1-scwrl ReadConformPDB servers/ABIpro_TS2.pdb NameConform ABIpro_TS2 SCWRLConform NameConform ABIpro_TS2-scwrl ReadConformPDB servers/ABIpro_TS3.pdb NameConform ABIpro_TS3 SCWRLConform NameConform ABIpro_TS3-scwrl ReadConformPDB servers/ABIpro_TS4.pdb NameConform ABIpro_TS4 SCWRLConform NameConform ABIpro_TS4-scwrl ReadConformPDB servers/ABIpro_TS5.pdb NameConform ABIpro_TS5 SCWRLConform NameConform ABIpro_TS5-scwrl ReadConformPDB servers/BayesHH_TS1.pdb NameConform BayesHH_TS1 SCWRLConform NameConform BayesHH_TS1-scwrl ReadConformPDB servers/Bilab-ENABLE_TS1.pdb NameConform Bilab-ENABLE_TS1 SCWRLConform NameConform Bilab-ENABLE_TS1-scwrl ReadConformPDB servers/Bilab-ENABLE_TS2.pdb NameConform Bilab-ENABLE_TS2 SCWRLConform NameConform Bilab-ENABLE_TS2-scwrl ReadConformPDB servers/Bilab-ENABLE_TS3.pdb NameConform Bilab-ENABLE_TS3 SCWRLConform NameConform Bilab-ENABLE_TS3-scwrl ReadConformPDB servers/Bilab-ENABLE_TS4.pdb NameConform Bilab-ENABLE_TS4 SCWRLConform NameConform Bilab-ENABLE_TS4-scwrl ReadConformPDB servers/Bilab-ENABLE_TS5.pdb NameConform Bilab-ENABLE_TS5 SCWRLConform NameConform Bilab-ENABLE_TS5-scwrl ReadConformPDB servers/CIRCLE_TS1.pdb NameConform CIRCLE_TS1 SCWRLConform NameConform CIRCLE_TS1-scwrl ReadConformPDB servers/CIRCLE_TS2.pdb NameConform CIRCLE_TS2 SCWRLConform NameConform CIRCLE_TS2-scwrl ReadConformPDB servers/CIRCLE_TS3.pdb NameConform CIRCLE_TS3 SCWRLConform NameConform CIRCLE_TS3-scwrl ReadConformPDB servers/CIRCLE_TS4.pdb NameConform CIRCLE_TS4 SCWRLConform NameConform CIRCLE_TS4-scwrl ReadConformPDB servers/CIRCLE_TS5.pdb NameConform CIRCLE_TS5 SCWRLConform NameConform CIRCLE_TS5-scwrl ReadConformPDB servers/CPHmodels_TS1.pdb NameConform CPHmodels_TS1 SCWRLConform NameConform CPHmodels_TS1-scwrl ReadConformPDB servers/CaspIta-FOX_TS1.pdb NameConform CaspIta-FOX_TS1 SCWRLConform NameConform CaspIta-FOX_TS1-scwrl ReadConformPDB servers/CaspIta-FOX_TS2.pdb NameConform CaspIta-FOX_TS2 SCWRLConform NameConform CaspIta-FOX_TS2-scwrl ReadConformPDB servers/CaspIta-FOX_TS3.pdb NameConform CaspIta-FOX_TS3 SCWRLConform NameConform CaspIta-FOX_TS3-scwrl ReadConformPDB servers/CaspIta-FOX_TS4.pdb NameConform CaspIta-FOX_TS4 SCWRLConform NameConform CaspIta-FOX_TS4-scwrl ReadConformPDB servers/CaspIta-FOX_TS5.pdb NameConform CaspIta-FOX_TS5 SCWRLConform NameConform CaspIta-FOX_TS5-scwrl ReadConformPDB servers/Distill_TS1.pdb NameConform Distill_TS1 SCWRLConform NameConform Distill_TS1-scwrl ReadConformPDB servers/Distill_TS2.pdb NameConform Distill_TS2 SCWRLConform NameConform Distill_TS2-scwrl ReadConformPDB servers/Distill_TS3.pdb NameConform Distill_TS3 SCWRLConform NameConform Distill_TS3-scwrl ReadConformPDB servers/Distill_TS4.pdb NameConform Distill_TS4 SCWRLConform NameConform Distill_TS4-scwrl ReadConformPDB servers/Distill_TS5.pdb NameConform Distill_TS5 SCWRLConform NameConform Distill_TS5-scwrl ReadConformPDB servers/FAMSD_TS1.pdb NameConform FAMSD_TS1 SCWRLConform NameConform FAMSD_TS1-scwrl ReadConformPDB servers/FAMSD_TS2.pdb NameConform FAMSD_TS2 SCWRLConform NameConform FAMSD_TS2-scwrl ReadConformPDB servers/FAMSD_TS3.pdb NameConform FAMSD_TS3 SCWRLConform NameConform FAMSD_TS3-scwrl ReadConformPDB servers/FAMSD_TS4.pdb NameConform FAMSD_TS4 SCWRLConform NameConform FAMSD_TS4-scwrl ReadConformPDB servers/FAMSD_TS5.pdb NameConform FAMSD_TS5 SCWRLConform NameConform FAMSD_TS5-scwrl ReadConformPDB servers/FAMS_TS1.pdb NameConform FAMS_TS1 SCWRLConform NameConform FAMS_TS1-scwrl ReadConformPDB servers/FAMS_TS2.pdb NameConform FAMS_TS2 SCWRLConform NameConform FAMS_TS2-scwrl ReadConformPDB servers/FAMS_TS3.pdb NameConform FAMS_TS3 SCWRLConform NameConform FAMS_TS3-scwrl ReadConformPDB servers/FAMS_TS4.pdb NameConform FAMS_TS4 SCWRLConform NameConform FAMS_TS4-scwrl ReadConformPDB servers/FAMS_TS5.pdb NameConform FAMS_TS5 SCWRLConform NameConform FAMS_TS5-scwrl ReadConformPDB servers/FOLDpro_TS1.pdb NameConform FOLDpro_TS1 SCWRLConform NameConform FOLDpro_TS1-scwrl ReadConformPDB servers/FOLDpro_TS2.pdb NameConform FOLDpro_TS2 SCWRLConform NameConform FOLDpro_TS2-scwrl ReadConformPDB servers/FOLDpro_TS3.pdb NameConform FOLDpro_TS3 SCWRLConform NameConform FOLDpro_TS3-scwrl ReadConformPDB servers/FOLDpro_TS4.pdb NameConform FOLDpro_TS4 SCWRLConform NameConform FOLDpro_TS4-scwrl ReadConformPDB servers/FOLDpro_TS5.pdb NameConform FOLDpro_TS5 SCWRLConform NameConform FOLDpro_TS5-scwrl ReadConformPDB servers/FORTE1_AL1.pdb NameConform FORTE1_AL1 SCWRLConform NameConform FORTE1_AL1-scwrl ReadConformPDB servers/FORTE1_AL2.pdb NameConform FORTE1_AL2 SCWRLConform NameConform FORTE1_AL2-scwrl ReadConformPDB servers/FORTE1_AL3.pdb NameConform FORTE1_AL3 SCWRLConform NameConform FORTE1_AL3-scwrl ReadConformPDB servers/FORTE1_AL4.pdb NameConform FORTE1_AL4 SCWRLConform NameConform FORTE1_AL4-scwrl ReadConformPDB servers/FORTE1_AL5.pdb NameConform FORTE1_AL5 SCWRLConform NameConform FORTE1_AL5-scwrl ReadConformPDB servers/FORTE2_AL1.pdb NameConform FORTE2_AL1 SCWRLConform NameConform FORTE2_AL1-scwrl ReadConformPDB servers/FORTE2_AL2.pdb NameConform FORTE2_AL2 SCWRLConform NameConform FORTE2_AL2-scwrl ReadConformPDB servers/FORTE2_AL3.pdb NameConform FORTE2_AL3 SCWRLConform NameConform FORTE2_AL3-scwrl ReadConformPDB servers/FORTE2_AL4.pdb NameConform FORTE2_AL4 SCWRLConform NameConform FORTE2_AL4-scwrl ReadConformPDB servers/FORTE2_AL5.pdb NameConform FORTE2_AL5 SCWRLConform NameConform FORTE2_AL5-scwrl ReadConformPDB servers/FPSOLVER-SERVER_TS1.pdb NameConform FPSOLVER-SERVER_TS1 SCWRLConform NameConform FPSOLVER-SERVER_TS1-scwrl ReadConformPDB servers/FPSOLVER-SERVER_TS2.pdb NameConform FPSOLVER-SERVER_TS2 SCWRLConform NameConform FPSOLVER-SERVER_TS2-scwrl ReadConformPDB servers/FPSOLVER-SERVER_TS3.pdb NameConform FPSOLVER-SERVER_TS3 SCWRLConform NameConform FPSOLVER-SERVER_TS3-scwrl ReadConformPDB servers/FPSOLVER-SERVER_TS4.pdb NameConform FPSOLVER-SERVER_TS4 SCWRLConform NameConform FPSOLVER-SERVER_TS4-scwrl ReadConformPDB servers/FPSOLVER-SERVER_TS5.pdb NameConform FPSOLVER-SERVER_TS5 SCWRLConform NameConform FPSOLVER-SERVER_TS5-scwrl ReadConformPDB servers/FUGMOD_TS1.pdb NameConform FUGMOD_TS1 SCWRLConform NameConform FUGMOD_TS1-scwrl ReadConformPDB servers/FUGMOD_TS2.pdb NameConform FUGMOD_TS2 SCWRLConform NameConform FUGMOD_TS2-scwrl ReadConformPDB servers/FUGMOD_TS3.pdb NameConform FUGMOD_TS3 SCWRLConform NameConform FUGMOD_TS3-scwrl ReadConformPDB servers/FUGMOD_TS4.pdb NameConform FUGMOD_TS4 SCWRLConform NameConform FUGMOD_TS4-scwrl ReadConformPDB servers/FUGMOD_TS5.pdb NameConform FUGMOD_TS5 SCWRLConform NameConform FUGMOD_TS5-scwrl ReadConformPDB servers/FUGUE_AL1.pdb NameConform FUGUE_AL1 SCWRLConform NameConform FUGUE_AL1-scwrl ReadConformPDB servers/FUGUE_AL2.pdb NameConform FUGUE_AL2 SCWRLConform NameConform FUGUE_AL2-scwrl ReadConformPDB servers/FUGUE_AL3.pdb NameConform FUGUE_AL3 SCWRLConform NameConform FUGUE_AL3-scwrl ReadConformPDB servers/FUGUE_AL4.pdb NameConform FUGUE_AL4 SCWRLConform NameConform FUGUE_AL4-scwrl ReadConformPDB servers/FUGUE_AL5.pdb NameConform FUGUE_AL5 SCWRLConform NameConform FUGUE_AL5-scwrl ReadConformPDB servers/FUNCTION_TS1.pdb NameConform FUNCTION_TS1 SCWRLConform NameConform FUNCTION_TS1-scwrl ReadConformPDB servers/FUNCTION_TS2.pdb NameConform FUNCTION_TS2 SCWRLConform NameConform FUNCTION_TS2-scwrl ReadConformPDB servers/FUNCTION_TS3.pdb NameConform FUNCTION_TS3 SCWRLConform NameConform FUNCTION_TS3-scwrl ReadConformPDB servers/FUNCTION_TS4.pdb NameConform FUNCTION_TS4 SCWRLConform NameConform FUNCTION_TS4-scwrl ReadConformPDB servers/FUNCTION_TS5.pdb NameConform FUNCTION_TS5 SCWRLConform NameConform FUNCTION_TS5-scwrl ReadConformPDB servers/Frankenstein_TS1.pdb NameConform Frankenstein_TS1 SCWRLConform NameConform Frankenstein_TS1-scwrl ReadConformPDB servers/Frankenstein_TS2.pdb NameConform Frankenstein_TS2 SCWRLConform NameConform Frankenstein_TS2-scwrl ReadConformPDB servers/Frankenstein_TS3.pdb NameConform Frankenstein_TS3 SCWRLConform NameConform Frankenstein_TS3-scwrl ReadConformPDB servers/GeneSilicoMetaServer_TS1.pdb NameConform GeneSilicoMetaServer_TS1 SCWRLConform NameConform GeneSilicoMetaServer_TS1-scwrl ReadConformPDB servers/GeneSilicoMetaServer_TS2.pdb NameConform GeneSilicoMetaServer_TS2 SCWRLConform NameConform GeneSilicoMetaServer_TS2-scwrl ReadConformPDB servers/GeneSilicoMetaServer_TS3.pdb NameConform GeneSilicoMetaServer_TS3 SCWRLConform NameConform GeneSilicoMetaServer_TS3-scwrl ReadConformPDB servers/GeneSilicoMetaServer_TS4.pdb NameConform GeneSilicoMetaServer_TS4 SCWRLConform NameConform GeneSilicoMetaServer_TS4-scwrl ReadConformPDB servers/GeneSilicoMetaServer_TS5.pdb NameConform GeneSilicoMetaServer_TS5 SCWRLConform NameConform GeneSilicoMetaServer_TS5-scwrl ReadConformPDB servers/HHpred1_TS1.pdb NameConform HHpred1_TS1 SCWRLConform NameConform HHpred1_TS1-scwrl ReadConformPDB servers/HHpred2_TS1.pdb NameConform HHpred2_TS1 SCWRLConform NameConform HHpred2_TS1-scwrl ReadConformPDB servers/HHpred3_TS1.pdb NameConform HHpred3_TS1 SCWRLConform NameConform HHpred3_TS1-scwrl ReadConformPDB servers/Huber-Torda-Server_TS1.pdb NameConform Huber-Torda-Server_TS1 SCWRLConform NameConform Huber-Torda-Server_TS1-scwrl ReadConformPDB servers/Huber-Torda-Server_TS2.pdb NameConform Huber-Torda-Server_TS2 SCWRLConform NameConform Huber-Torda-Server_TS2-scwrl ReadConformPDB servers/Huber-Torda-Server_TS3.pdb NameConform Huber-Torda-Server_TS3 SCWRLConform NameConform Huber-Torda-Server_TS3-scwrl ReadConformPDB servers/Huber-Torda-Server_TS4.pdb NameConform Huber-Torda-Server_TS4 SCWRLConform NameConform Huber-Torda-Server_TS4-scwrl ReadConformPDB servers/Huber-Torda-Server_TS5.pdb NameConform Huber-Torda-Server_TS5 SCWRLConform NameConform Huber-Torda-Server_TS5-scwrl ReadConformPDB servers/LOOPP_TS1.pdb NameConform LOOPP_TS1 SCWRLConform NameConform LOOPP_TS1-scwrl ReadConformPDB servers/LOOPP_TS2.pdb NameConform LOOPP_TS2 SCWRLConform NameConform LOOPP_TS2-scwrl ReadConformPDB servers/LOOPP_TS3.pdb NameConform LOOPP_TS3 SCWRLConform NameConform LOOPP_TS3-scwrl ReadConformPDB servers/LOOPP_TS4.pdb NameConform LOOPP_TS4 SCWRLConform NameConform LOOPP_TS4-scwrl ReadConformPDB servers/LOOPP_TS5.pdb NameConform LOOPP_TS5 SCWRLConform NameConform LOOPP_TS5-scwrl ReadConformPDB servers/MIG_FROST_AL1.pdb NameConform MIG_FROST_AL1 SCWRLConform NameConform MIG_FROST_AL1-scwrl ReadConformPDB servers/Ma-OPUS-server_TS1.pdb NameConform Ma-OPUS-server_TS1 SCWRLConform NameConform Ma-OPUS-server_TS1-scwrl ReadConformPDB servers/Ma-OPUS-server_TS2.pdb NameConform Ma-OPUS-server_TS2 SCWRLConform NameConform Ma-OPUS-server_TS2-scwrl ReadConformPDB servers/Ma-OPUS-server_TS3.pdb NameConform Ma-OPUS-server_TS3 SCWRLConform NameConform Ma-OPUS-server_TS3-scwrl ReadConformPDB servers/Ma-OPUS-server_TS4.pdb NameConform Ma-OPUS-server_TS4 SCWRLConform NameConform Ma-OPUS-server_TS4-scwrl ReadConformPDB servers/Ma-OPUS-server_TS5.pdb NameConform Ma-OPUS-server_TS5 SCWRLConform NameConform Ma-OPUS-server_TS5-scwrl ReadConformPDB servers/MetaTasser_TS1.pdb NameConform MetaTasser_TS1 SCWRLConform NameConform MetaTasser_TS1-scwrl ReadConformPDB servers/MetaTasser_TS2.pdb NameConform MetaTasser_TS2 SCWRLConform NameConform MetaTasser_TS2-scwrl ReadConformPDB servers/MetaTasser_TS3.pdb NameConform MetaTasser_TS3 SCWRLConform NameConform MetaTasser_TS3-scwrl ReadConformPDB servers/MetaTasser_TS4.pdb NameConform MetaTasser_TS4 SCWRLConform NameConform MetaTasser_TS4-scwrl ReadConformPDB servers/MetaTasser_TS5.pdb NameConform MetaTasser_TS5 SCWRLConform NameConform MetaTasser_TS5-scwrl ReadConformPDB servers/NN_PUT_lab_TS1.pdb NameConform NN_PUT_lab_TS1 SCWRLConform NameConform NN_PUT_lab_TS1-scwrl ReadConformPDB servers/PROTINFO-AB_TS1.pdb NameConform PROTINFO-AB_TS1 SCWRLConform NameConform PROTINFO-AB_TS1-scwrl ReadConformPDB servers/PROTINFO-AB_TS2.pdb NameConform PROTINFO-AB_TS2 SCWRLConform NameConform PROTINFO-AB_TS2-scwrl ReadConformPDB servers/PROTINFO-AB_TS3.pdb NameConform PROTINFO-AB_TS3 SCWRLConform NameConform PROTINFO-AB_TS3-scwrl ReadConformPDB servers/PROTINFO-AB_TS4.pdb NameConform PROTINFO-AB_TS4 SCWRLConform NameConform PROTINFO-AB_TS4-scwrl ReadConformPDB servers/PROTINFO-AB_TS5.pdb NameConform PROTINFO-AB_TS5 SCWRLConform NameConform PROTINFO-AB_TS5-scwrl ReadConformPDB servers/PROTINFO_TS1.pdb NameConform PROTINFO_TS1 SCWRLConform NameConform PROTINFO_TS1-scwrl ReadConformPDB servers/PROTINFO_TS2.pdb NameConform PROTINFO_TS2 SCWRLConform NameConform PROTINFO_TS2-scwrl ReadConformPDB servers/PROTINFO_TS3.pdb NameConform PROTINFO_TS3 SCWRLConform NameConform PROTINFO_TS3-scwrl ReadConformPDB servers/PROTINFO_TS4.pdb NameConform PROTINFO_TS4 SCWRLConform NameConform PROTINFO_TS4-scwrl ReadConformPDB servers/PROTINFO_TS5.pdb NameConform PROTINFO_TS5 SCWRLConform NameConform PROTINFO_TS5-scwrl ReadConformPDB servers/Pcons6_TS1.pdb NameConform Pcons6_TS1 SCWRLConform NameConform Pcons6_TS1-scwrl ReadConformPDB servers/Pcons6_TS2.pdb NameConform Pcons6_TS2 SCWRLConform NameConform Pcons6_TS2-scwrl ReadConformPDB servers/Pcons6_TS3.pdb NameConform Pcons6_TS3 SCWRLConform NameConform Pcons6_TS3-scwrl ReadConformPDB servers/Pcons6_TS4.pdb NameConform Pcons6_TS4 SCWRLConform NameConform Pcons6_TS4-scwrl ReadConformPDB servers/Pcons6_TS5.pdb NameConform Pcons6_TS5 SCWRLConform NameConform Pcons6_TS5-scwrl ReadConformPDB servers/Phyre-1_TS1.pdb NameConform Phyre-1_TS1 SCWRLConform NameConform Phyre-1_TS1-scwrl ReadConformPDB servers/Phyre-2_TS1.pdb NameConform Phyre-2_TS1 SCWRLConform NameConform Phyre-2_TS1-scwrl ReadConformPDB servers/Phyre-2_TS2.pdb NameConform Phyre-2_TS2 SCWRLConform NameConform Phyre-2_TS2-scwrl ReadConformPDB servers/Phyre-2_TS3.pdb NameConform Phyre-2_TS3 SCWRLConform NameConform Phyre-2_TS3-scwrl ReadConformPDB servers/Phyre-2_TS4.pdb NameConform Phyre-2_TS4 SCWRLConform NameConform Phyre-2_TS4-scwrl ReadConformPDB servers/Phyre-2_TS5.pdb NameConform Phyre-2_TS5 SCWRLConform NameConform Phyre-2_TS5-scwrl ReadConformPDB servers/Pmodeller6_TS1.pdb NameConform Pmodeller6_TS1 SCWRLConform NameConform Pmodeller6_TS1-scwrl ReadConformPDB servers/Pmodeller6_TS2.pdb NameConform Pmodeller6_TS2 SCWRLConform NameConform Pmodeller6_TS2-scwrl ReadConformPDB servers/Pmodeller6_TS3.pdb NameConform Pmodeller6_TS3 SCWRLConform NameConform Pmodeller6_TS3-scwrl ReadConformPDB servers/Pmodeller6_TS4.pdb NameConform Pmodeller6_TS4 SCWRLConform NameConform Pmodeller6_TS4-scwrl ReadConformPDB servers/Pmodeller6_TS5.pdb NameConform Pmodeller6_TS5 SCWRLConform NameConform Pmodeller6_TS5-scwrl ReadConformPDB servers/RAPTOR-ACE_TS1.pdb NameConform RAPTOR-ACE_TS1 SCWRLConform NameConform RAPTOR-ACE_TS1-scwrl ReadConformPDB servers/RAPTOR-ACE_TS2.pdb NameConform RAPTOR-ACE_TS2 SCWRLConform NameConform RAPTOR-ACE_TS2-scwrl ReadConformPDB servers/RAPTOR-ACE_TS3.pdb NameConform RAPTOR-ACE_TS3 SCWRLConform NameConform RAPTOR-ACE_TS3-scwrl ReadConformPDB servers/RAPTOR-ACE_TS4.pdb NameConform RAPTOR-ACE_TS4 SCWRLConform NameConform RAPTOR-ACE_TS4-scwrl ReadConformPDB servers/RAPTOR-ACE_TS5.pdb NameConform RAPTOR-ACE_TS5 SCWRLConform NameConform RAPTOR-ACE_TS5-scwrl ReadConformPDB servers/RAPTORESS_TS1.pdb NameConform RAPTORESS_TS1 SCWRLConform NameConform RAPTORESS_TS1-scwrl ReadConformPDB servers/RAPTORESS_TS2.pdb NameConform RAPTORESS_TS2 SCWRLConform NameConform RAPTORESS_TS2-scwrl ReadConformPDB servers/RAPTORESS_TS3.pdb NameConform RAPTORESS_TS3 SCWRLConform NameConform RAPTORESS_TS3-scwrl ReadConformPDB servers/RAPTORESS_TS4.pdb NameConform RAPTORESS_TS4 SCWRLConform NameConform RAPTORESS_TS4-scwrl ReadConformPDB servers/RAPTORESS_TS5.pdb NameConform RAPTORESS_TS5 SCWRLConform NameConform RAPTORESS_TS5-scwrl ReadConformPDB servers/RAPTOR_TS1.pdb NameConform RAPTOR_TS1 SCWRLConform NameConform RAPTOR_TS1-scwrl ReadConformPDB servers/RAPTOR_TS2.pdb NameConform RAPTOR_TS2 SCWRLConform NameConform RAPTOR_TS2-scwrl ReadConformPDB servers/RAPTOR_TS3.pdb NameConform RAPTOR_TS3 SCWRLConform NameConform RAPTOR_TS3-scwrl ReadConformPDB servers/RAPTOR_TS4.pdb NameConform RAPTOR_TS4 SCWRLConform NameConform RAPTOR_TS4-scwrl ReadConformPDB servers/RAPTOR_TS5.pdb NameConform RAPTOR_TS5 SCWRLConform NameConform RAPTOR_TS5-scwrl ReadConformPDB servers/ROBETTA_TS1.pdb NameConform ROBETTA_TS1 SCWRLConform NameConform ROBETTA_TS1-scwrl ReadConformPDB servers/ROBETTA_TS2.pdb NameConform ROBETTA_TS2 SCWRLConform NameConform ROBETTA_TS2-scwrl ReadConformPDB servers/ROBETTA_TS3.pdb NameConform ROBETTA_TS3 SCWRLConform NameConform ROBETTA_TS3-scwrl ReadConformPDB servers/ROBETTA_TS4.pdb NameConform ROBETTA_TS4 SCWRLConform NameConform ROBETTA_TS4-scwrl ReadConformPDB servers/ROBETTA_TS5.pdb NameConform ROBETTA_TS5 SCWRLConform NameConform ROBETTA_TS5-scwrl ReadConformPDB servers/ROKKY_TS1.pdb NameConform ROKKY_TS1 SCWRLConform NameConform ROKKY_TS1-scwrl ReadConformPDB servers/ROKKY_TS2.pdb NameConform ROKKY_TS2 SCWRLConform NameConform ROKKY_TS2-scwrl ReadConformPDB servers/SAM-T02_AL1.pdb NameConform SAM-T02_AL1 SCWRLConform NameConform SAM-T02_AL1-scwrl ReadConformPDB servers/SAM-T02_AL2.pdb NameConform SAM-T02_AL2 SCWRLConform NameConform SAM-T02_AL2-scwrl ReadConformPDB servers/SAM-T02_AL3.pdb NameConform SAM-T02_AL3 SCWRLConform NameConform SAM-T02_AL3-scwrl ReadConformPDB servers/SAM-T02_AL4.pdb NameConform SAM-T02_AL4 SCWRLConform NameConform SAM-T02_AL4-scwrl ReadConformPDB servers/SAM-T02_AL5.pdb NameConform SAM-T02_AL5 SCWRLConform NameConform SAM-T02_AL5-scwrl ReadConformPDB servers/SAM-T99_AL1.pdb NameConform SAM-T99_AL1 SCWRLConform NameConform SAM-T99_AL1-scwrl ReadConformPDB servers/SAM-T99_AL2.pdb NameConform SAM-T99_AL2 SCWRLConform NameConform SAM-T99_AL2-scwrl ReadConformPDB servers/SAM-T99_AL3.pdb NameConform SAM-T99_AL3 SCWRLConform NameConform SAM-T99_AL3-scwrl ReadConformPDB servers/SAM-T99_AL4.pdb NameConform SAM-T99_AL4 SCWRLConform NameConform SAM-T99_AL4-scwrl ReadConformPDB servers/SAM-T99_AL5.pdb NameConform SAM-T99_AL5 SCWRLConform NameConform SAM-T99_AL5-scwrl ReadConformPDB servers/SAM_T06_server_TS1.pdb NameConform SAM_T06_server_TS1 SCWRLConform NameConform SAM_T06_server_TS1-scwrl ReadConformPDB servers/SAM_T06_server_TS2.pdb NameConform SAM_T06_server_TS2 SCWRLConform NameConform SAM_T06_server_TS2-scwrl ReadConformPDB servers/SAM_T06_server_TS3.pdb NameConform SAM_T06_server_TS3 SCWRLConform NameConform SAM_T06_server_TS3-scwrl ReadConformPDB servers/SAM_T06_server_TS4.pdb NameConform SAM_T06_server_TS4 SCWRLConform NameConform SAM_T06_server_TS4-scwrl ReadConformPDB servers/SAM_T06_server_TS5.pdb NameConform SAM_T06_server_TS5 SCWRLConform NameConform SAM_T06_server_TS5-scwrl ReadConformPDB servers/SP3_TS1.pdb NameConform SP3_TS1 SCWRLConform NameConform SP3_TS1-scwrl ReadConformPDB servers/SP3_TS2.pdb NameConform SP3_TS2 SCWRLConform NameConform SP3_TS2-scwrl ReadConformPDB servers/SP3_TS3.pdb NameConform SP3_TS3 SCWRLConform NameConform SP3_TS3-scwrl ReadConformPDB servers/SP3_TS4.pdb NameConform SP3_TS4 SCWRLConform NameConform SP3_TS4-scwrl ReadConformPDB servers/SP3_TS5.pdb NameConform SP3_TS5 SCWRLConform NameConform SP3_TS5-scwrl ReadConformPDB servers/SP4_TS1.pdb NameConform SP4_TS1 SCWRLConform NameConform SP4_TS1-scwrl ReadConformPDB servers/SP4_TS2.pdb NameConform SP4_TS2 SCWRLConform NameConform SP4_TS2-scwrl ReadConformPDB servers/SP4_TS3.pdb NameConform SP4_TS3 SCWRLConform NameConform SP4_TS3-scwrl ReadConformPDB servers/SP4_TS4.pdb NameConform SP4_TS4 SCWRLConform NameConform SP4_TS4-scwrl ReadConformPDB servers/SP4_TS5.pdb NameConform SP4_TS5 SCWRLConform NameConform SP4_TS5-scwrl ReadConformPDB servers/SPARKS2_TS1.pdb NameConform SPARKS2_TS1 SCWRLConform NameConform SPARKS2_TS1-scwrl ReadConformPDB servers/SPARKS2_TS2.pdb NameConform SPARKS2_TS2 SCWRLConform NameConform SPARKS2_TS2-scwrl ReadConformPDB servers/SPARKS2_TS3.pdb NameConform SPARKS2_TS3 SCWRLConform NameConform SPARKS2_TS3-scwrl ReadConformPDB servers/SPARKS2_TS4.pdb NameConform SPARKS2_TS4 SCWRLConform NameConform SPARKS2_TS4-scwrl ReadConformPDB servers/SPARKS2_TS5.pdb NameConform SPARKS2_TS5 SCWRLConform NameConform SPARKS2_TS5-scwrl ReadConformPDB servers/UNI-EID_bnmx_TS1.pdb NameConform UNI-EID_bnmx_TS1 SCWRLConform NameConform UNI-EID_bnmx_TS1-scwrl ReadConformPDB servers/UNI-EID_bnmx_TS2.pdb NameConform UNI-EID_bnmx_TS2 SCWRLConform NameConform UNI-EID_bnmx_TS2-scwrl ReadConformPDB servers/UNI-EID_bnmx_TS3.pdb NameConform UNI-EID_bnmx_TS3 SCWRLConform NameConform UNI-EID_bnmx_TS3-scwrl ReadConformPDB servers/UNI-EID_bnmx_TS4.pdb NameConform UNI-EID_bnmx_TS4 SCWRLConform NameConform UNI-EID_bnmx_TS4-scwrl ReadConformPDB servers/UNI-EID_bnmx_TS5.pdb NameConform UNI-EID_bnmx_TS5 SCWRLConform NameConform UNI-EID_bnmx_TS5-scwrl ReadConformPDB servers/UNI-EID_expm_TS1.pdb NameConform UNI-EID_expm_TS1 SCWRLConform NameConform UNI-EID_expm_TS1-scwrl ReadConformPDB servers/UNI-EID_sfst_AL1.pdb NameConform UNI-EID_sfst_AL1 SCWRLConform NameConform UNI-EID_sfst_AL1-scwrl ReadConformPDB servers/UNI-EID_sfst_AL2.pdb NameConform UNI-EID_sfst_AL2 SCWRLConform NameConform UNI-EID_sfst_AL2-scwrl ReadConformPDB servers/UNI-EID_sfst_AL3.pdb NameConform UNI-EID_sfst_AL3 SCWRLConform NameConform UNI-EID_sfst_AL3-scwrl ReadConformPDB servers/UNI-EID_sfst_AL4.pdb NameConform UNI-EID_sfst_AL4 SCWRLConform NameConform UNI-EID_sfst_AL4-scwrl ReadConformPDB servers/UNI-EID_sfst_AL5.pdb NameConform UNI-EID_sfst_AL5 SCWRLConform NameConform UNI-EID_sfst_AL5-scwrl ReadConformPDB servers/Zhang-Server_TS1.pdb NameConform Zhang-Server_TS1 SCWRLConform NameConform Zhang-Server_TS1-scwrl ReadConformPDB servers/Zhang-Server_TS2.pdb NameConform Zhang-Server_TS2 SCWRLConform NameConform Zhang-Server_TS2-scwrl ReadConformPDB servers/Zhang-Server_TS3.pdb NameConform Zhang-Server_TS3 SCWRLConform NameConform Zhang-Server_TS3-scwrl ReadConformPDB servers/Zhang-Server_TS4.pdb NameConform Zhang-Server_TS4 SCWRLConform NameConform Zhang-Server_TS4-scwrl ReadConformPDB servers/Zhang-Server_TS5.pdb NameConform Zhang-Server_TS5 SCWRLConform NameConform Zhang-Server_TS5-scwrl ReadConformPDB servers/beautshot_TS1.pdb NameConform beautshot_TS1 SCWRLConform NameConform beautshot_TS1-scwrl ReadConformPDB servers/beautshotbase_TS1.pdb NameConform beautshotbase_TS1 SCWRLConform NameConform beautshotbase_TS1-scwrl ReadConformPDB servers/forecast-s_AL1.pdb NameConform forecast-s_AL1 SCWRLConform NameConform forecast-s_AL1-scwrl ReadConformPDB servers/forecast-s_AL2.pdb NameConform forecast-s_AL2 SCWRLConform NameConform forecast-s_AL2-scwrl ReadConformPDB servers/forecast-s_AL3.pdb NameConform forecast-s_AL3 SCWRLConform NameConform forecast-s_AL3-scwrl ReadConformPDB servers/forecast-s_AL4.pdb NameConform forecast-s_AL4 SCWRLConform NameConform forecast-s_AL4-scwrl ReadConformPDB servers/forecast-s_AL5.pdb NameConform forecast-s_AL5 SCWRLConform NameConform forecast-s_AL5-scwrl ReadConformPDB servers/gtg_AL1.pdb NameConform gtg_AL1 SCWRLConform NameConform gtg_AL1-scwrl ReadConformPDB servers/gtg_AL2.pdb NameConform gtg_AL2 SCWRLConform NameConform gtg_AL2-scwrl ReadConformPDB servers/gtg_AL3.pdb NameConform gtg_AL3 SCWRLConform NameConform gtg_AL3-scwrl ReadConformPDB servers/gtg_AL4.pdb NameConform gtg_AL4 SCWRLConform NameConform gtg_AL4-scwrl ReadConformPDB servers/gtg_AL5.pdb NameConform gtg_AL5 SCWRLConform NameConform gtg_AL5-scwrl ReadConformPDB servers/karypis.srv.2_TS1.pdb NameConform karypis.srv.2_TS1 SCWRLConform NameConform karypis.srv.2_TS1-scwrl ReadConformPDB servers/karypis.srv.2_TS2.pdb NameConform karypis.srv.2_TS2 SCWRLConform NameConform karypis.srv.2_TS2-scwrl ReadConformPDB servers/karypis.srv.2_TS3.pdb NameConform karypis.srv.2_TS3 SCWRLConform NameConform karypis.srv.2_TS3-scwrl ReadConformPDB servers/karypis.srv.2_TS4.pdb NameConform karypis.srv.2_TS4 SCWRLConform NameConform karypis.srv.2_TS4-scwrl ReadConformPDB servers/karypis.srv.2_TS5.pdb NameConform karypis.srv.2_TS5 SCWRLConform NameConform karypis.srv.2_TS5-scwrl ReadConformPDB servers/karypis.srv.4_TS1.pdb NameConform karypis.srv.4_TS1 SCWRLConform NameConform karypis.srv.4_TS1-scwrl ReadConformPDB servers/karypis.srv.4_TS2.pdb NameConform karypis.srv.4_TS2 SCWRLConform NameConform karypis.srv.4_TS2-scwrl ReadConformPDB servers/karypis.srv.4_TS3.pdb NameConform karypis.srv.4_TS3 SCWRLConform NameConform karypis.srv.4_TS3-scwrl ReadConformPDB servers/karypis.srv.4_TS4.pdb NameConform karypis.srv.4_TS4 SCWRLConform NameConform karypis.srv.4_TS4-scwrl ReadConformPDB servers/karypis.srv.4_TS5.pdb NameConform karypis.srv.4_TS5 SCWRLConform NameConform karypis.srv.4_TS5-scwrl ReadConformPDB servers/karypis.srv_TS1.pdb NameConform karypis.srv_TS1 SCWRLConform NameConform karypis.srv_TS1-scwrl ReadConformPDB servers/karypis.srv_TS2.pdb NameConform karypis.srv_TS2 SCWRLConform NameConform karypis.srv_TS2-scwrl ReadConformPDB servers/karypis.srv_TS3.pdb NameConform karypis.srv_TS3 SCWRLConform NameConform karypis.srv_TS3-scwrl ReadConformPDB servers/karypis.srv_TS4.pdb NameConform karypis.srv_TS4 SCWRLConform NameConform karypis.srv_TS4-scwrl ReadConformPDB servers/karypis.srv_TS5.pdb NameConform karypis.srv_TS5 SCWRLConform NameConform karypis.srv_TS5-scwrl ReadConformPDB servers/keasar-server_TS1.pdb NameConform keasar-server_TS1 SCWRLConform NameConform keasar-server_TS1-scwrl ReadConformPDB servers/keasar-server_TS2.pdb NameConform keasar-server_TS2 SCWRLConform NameConform keasar-server_TS2-scwrl ReadConformPDB servers/keasar-server_TS3.pdb NameConform keasar-server_TS3 SCWRLConform NameConform keasar-server_TS3-scwrl ReadConformPDB servers/keasar-server_TS4.pdb NameConform keasar-server_TS4 SCWRLConform NameConform keasar-server_TS4-scwrl ReadConformPDB servers/keasar-server_TS5.pdb NameConform keasar-server_TS5 SCWRLConform NameConform keasar-server_TS5-scwrl ReadConformPDB servers/mGen-3D_TS1.pdb NameConform mGen-3D_TS1 SCWRLConform NameConform mGen-3D_TS1-scwrl ReadConformPDB servers/nFOLD_TS1.pdb NameConform nFOLD_TS1 SCWRLConform NameConform nFOLD_TS1-scwrl ReadConformPDB servers/nFOLD_TS2.pdb NameConform nFOLD_TS2 SCWRLConform NameConform nFOLD_TS2-scwrl ReadConformPDB servers/nFOLD_TS3.pdb NameConform nFOLD_TS3 SCWRLConform NameConform nFOLD_TS3-scwrl ReadConformPDB servers/nFOLD_TS4.pdb NameConform nFOLD_TS4 SCWRLConform NameConform nFOLD_TS4-scwrl ReadConformPDB servers/nFOLD_TS5.pdb NameConform nFOLD_TS5 SCWRLConform NameConform nFOLD_TS5-scwrl ReadConformPDB servers/shub_TS1.pdb NameConform shub_TS1 SCWRLConform NameConform shub_TS1-scwrl CostConform Time // The following alignments are not as good as the ones tried above, // so are not used in getting the starting point. InFilePrefix ReadFragmentAlignment T0295.t2k.many.frag ReadFragmentAlignment T0295.t04.many.frag ReadFragmentAlignment T0295.t06.many.frag // The next 3 lines save the templates in a single file, to avoid having // to reread the PDB files. Note that ReadTemplateAtoms should be called // before any ReadFragmentAlignments to take full advantage of this // cached results. OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs \ HealPeptide 0.3 \ JiggleSubtree 0.3 \ JiggleSegment 0.3 \ OptSubtree 1 \ OptSegment 1 \ OptAllSegments 0.3 \ ShiftSubtree 0.3 \ ShiftSegment 0.3 \ TweakPhiSubtree 0.3 \ TweakPhiSegment 0.3 \ TweakPsiSubtree 0.3 \ TweakPsiSegment 0.3 \ TweakPsiPhiSubtree 0.3 \ TweakPsiPhiSegment 0.3 \ TweakHbondSubtree 0.3 \ TweakHbondSegment 0.3 \ TweakMultimer 0.3 \ TweakPeptide 0.3 \ OneRotamer 1 \ ClashingRotamer 1 \ ClusteredRotamer 2 \ ReduceBreak 5 \ CloseGap 5 \ HealGap 5 \ MoveGap 5 \ ReduceConstraint 5 \ ImproveSSBond 0 \ InsertSSBond 0 \ InsertAlignment 1 \ InsertSpecificFragment 5 \ InsertFragment 5 \ TwoFragment 5 \ CrossOver 3 \ CrossAndInsert 5 \ ReduceClash 5 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 3 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0295.try2-opt1 PrintConformPDB T0295.try2-opt1.pdb SCWRLConform NameConform T0295.try2-opt1-scwrl PrintConformPDB T0295.try2-opt1-scwrl.pdb CostConform Time InitMethodProbs \ OneRotamer 5 \ ClashingRotamer 1 \ ClusteredRotamer 1 \ CrossOver 1 \ CrossAndInsert 1\ CloseGap 1 \ MoveGap 1 \ HealGap 2 \ InsertFragment 1 \ InsertSpecificFragment 2 \ ReduceBreak 2 \ ReduceConstraint 2 \ ReduceClash 1 \ JiggleSegment 1 \ JiggleSubtree 1 \ OptAllSegments 1 \ OptSegment 1 \ OptSubtree 1 \ ShiftSegment 1 \ ShiftSubtree 1 \ TweakHbondSegment 1 \ TweakHbondSubtree 1 \ TweakPhiSegment 1 \ TweakPhiSubtree 1 \ TweakPsiSegment 1 \ TweakPsiSubtree 1 \ TweakPsiPhiSegment 1 \ TweakPsiPhiSubtree 1 CostConform OptConform pool_size 40 num_gen 60 gen_size 100 \ super_iter 2 super_num_gen 300 use_all NameConform T0295.try2-opt2 PrintConformPDB T0295.try2-opt2.pdb # PrintConformHbonds try2-opt2.all-hbonds # PrintConformHbonds nonhelix backbone try2-opt2.beta-hbonds PrintConformSheets try2-opt2.sheets PrintConformHelices try2-opt2.helices PrintConstraints all try2-opt2.constraints # PrintConformBreaks try2-opt2.breaks CostConform Time quit