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-40pc-3157.atoms # The rotamer library need not be from the same set of chains as the TrainingAtoms. # It encodes the most probable conformations of sidechain and backbone # for each residue type. ReadRotamerLibrary dunbrack-40pc-3157.rot Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix # ReadTargetPDB T0498.blank.pdb ReadTargetSeq T0498.a2m 1 NameTarget T0498 PopConform InFilePrefix include costfcn-init.under include try4.costfcn // Scale the break and clashe costs down, then gradually back up again ScaleCost break 0.25 soft_clashes 0.25 Time MakeGenericFragmentLibrary Time InFilePrefix ReadTemplateAtoms Template.atoms ReadFragmentAlignment fragment_only T0498.t2k.many.frag ReadFragmentAlignment fragment_only T0498.t04.many.frag ReadFragmentAlignment fragment_only T0498.t06.many.frag // Switch to the following (commenting out the TryAllAlign) // to polish existing models InfilePrefix decoys/ # include SAM-T08-MQAU.read_under ReadConformPDB servers/3D-JIGSAW_AEP_TS1 name 3D-JIGSAW_AEP_TS1 ReadConformPDB servers/3D-JIGSAW_AEP_TS2 name 3D-JIGSAW_AEP_TS2 ReadConformPDB servers/3D-JIGSAW_AEP_TS3 name 3D-JIGSAW_AEP_TS3 ReadConformPDB servers/3D-JIGSAW_AEP_TS4 name 3D-JIGSAW_AEP_TS4 ReadConformPDB servers/3D-JIGSAW_AEP_TS5 name 3D-JIGSAW_AEP_TS5 ReadConformPDB servers/3D-JIGSAW_V3_TS1 name 3D-JIGSAW_V3_TS1 ReadConformPDB servers/3D-JIGSAW_V3_TS2 name 3D-JIGSAW_V3_TS2 ReadConformPDB servers/3D-JIGSAW_V3_TS3 name 3D-JIGSAW_V3_TS3 ReadConformPDB servers/3D-JIGSAW_V3_TS4 name 3D-JIGSAW_V3_TS4 ReadConformPDB servers/3D-JIGSAW_V3_TS5 name 3D-JIGSAW_V3_TS5 ReadConformPDB servers/3DShot2_TS1 name 3DShot2_TS1 ReadConformPDB servers/3Dpro_TS1 name 3Dpro_TS1 ReadConformPDB servers/3Dpro_TS2 name 3Dpro_TS2 ReadConformPDB servers/3Dpro_TS3 name 3Dpro_TS3 ReadConformPDB servers/3Dpro_TS4 name 3Dpro_TS4 ReadConformPDB servers/3Dpro_TS5 name 3Dpro_TS5 ReadConformPDB servers/ACOMPMOD_TS1 name ACOMPMOD_TS1 ReadConformPDB servers/ACOMPMOD_TS2 name ACOMPMOD_TS2 ReadConformPDB servers/ACOMPMOD_TS3 name ACOMPMOD_TS3 ReadConformPDB servers/ACOMPMOD_TS4 name ACOMPMOD_TS4 ReadConformPDB servers/ACOMPMOD_TS5 name ACOMPMOD_TS5 ReadConformPDB servers/BAKER-ROBETTA_TS1 name BAKER-ROBETTA_TS1 ReadConformPDB servers/BAKER-ROBETTA_TS2 name BAKER-ROBETTA_TS2 ReadConformPDB servers/BAKER-ROBETTA_TS3 name BAKER-ROBETTA_TS3 ReadConformPDB servers/BAKER-ROBETTA_TS4 name BAKER-ROBETTA_TS4 ReadConformPDB servers/BAKER-ROBETTA_TS5 name BAKER-ROBETTA_TS5 ReadConformPDB servers/BioSerf_TS1 name BioSerf_TS1 ReadConformPDB servers/COMA-M_TS1 name COMA-M_TS1 ReadConformPDB servers/COMA-M_TS2 name COMA-M_TS2 ReadConformPDB servers/COMA-M_TS3 name COMA-M_TS3 ReadConformPDB servers/COMA-M_TS4 name COMA-M_TS4 ReadConformPDB servers/COMA-M_TS5 name COMA-M_TS5 ReadConformPDB servers/COMA_TS1 name COMA_TS1 ReadConformPDB servers/COMA_TS2 name COMA_TS2 ReadConformPDB servers/COMA_TS3 name COMA_TS3 ReadConformPDB servers/COMA_TS4 name COMA_TS4 ReadConformPDB servers/COMA_TS5 name COMA_TS5 ReadConformPDB servers/CpHModels_TS1 name CpHModels_TS1 ReadConformPDB servers/Distill_TS1 name Distill_TS1 ReadConformPDB servers/Distill_TS2 name Distill_TS2 ReadConformPDB servers/Distill_TS3 name Distill_TS3 ReadConformPDB servers/Distill_TS4 name Distill_TS4 ReadConformPDB servers/Distill_TS5 name Distill_TS5 ReadConformPDB servers/FALCON_CONSENSUS_TS1 name FALCON_CONSENSUS_TS1 ReadConformPDB servers/FALCON_CONSENSUS_TS2 name FALCON_CONSENSUS_TS2 ReadConformPDB servers/FALCON_CONSENSUS_TS3 name FALCON_CONSENSUS_TS3 ReadConformPDB servers/FALCON_CONSENSUS_TS4 name FALCON_CONSENSUS_TS4 ReadConformPDB servers/FALCON_CONSENSUS_TS5 name FALCON_CONSENSUS_TS5 ReadConformPDB servers/FALCON_TS1 name FALCON_TS1 ReadConformPDB servers/FALCON_TS2 name FALCON_TS2 ReadConformPDB servers/FALCON_TS3 name FALCON_TS3 ReadConformPDB servers/FALCON_TS4 name FALCON_TS4 ReadConformPDB servers/FALCON_TS5 name FALCON_TS5 ReadConformPDB servers/FAMSD_TS1 name FAMSD_TS1 ReadConformPDB servers/FAMSD_TS2 name FAMSD_TS2 ReadConformPDB servers/FAMSD_TS3 name FAMSD_TS3 ReadConformPDB servers/FAMSD_TS4 name FAMSD_TS4 ReadConformPDB servers/FAMSD_TS5 name FAMSD_TS5 ReadConformPDB servers/FEIG_TS1 name FEIG_TS1 ReadConformPDB servers/FEIG_TS2 name FEIG_TS2 ReadConformPDB servers/FEIG_TS3 name FEIG_TS3 ReadConformPDB servers/FEIG_TS4 name FEIG_TS4 ReadConformPDB servers/FEIG_TS5 name FEIG_TS5 ReadConformPDB servers/FFASflextemplate_TS1 name FFASflextemplate_TS1 ReadConformPDB servers/FFASflextemplate_TS2 name FFASflextemplate_TS2 ReadConformPDB servers/FFASflextemplate_TS3 name FFASflextemplate_TS3 ReadConformPDB servers/FFASflextemplate_TS4 name FFASflextemplate_TS4 ReadConformPDB servers/FFASflextemplate_TS5 name FFASflextemplate_TS5 ReadConformPDB servers/FFASstandard_TS1 name FFASstandard_TS1 ReadConformPDB servers/FFASstandard_TS2 name FFASstandard_TS2 ReadConformPDB servers/FFASstandard_TS3 name FFASstandard_TS3 ReadConformPDB servers/FFASstandard_TS4 name FFASstandard_TS4 ReadConformPDB servers/FFASstandard_TS5 name FFASstandard_TS5 ReadConformPDB servers/FFASsuboptimal_TS1 name FFASsuboptimal_TS1 ReadConformPDB servers/FFASsuboptimal_TS2 name FFASsuboptimal_TS2 ReadConformPDB servers/FFASsuboptimal_TS3 name FFASsuboptimal_TS3 ReadConformPDB servers/FFASsuboptimal_TS4 name FFASsuboptimal_TS4 ReadConformPDB servers/FFASsuboptimal_TS5 name FFASsuboptimal_TS5 ReadConformPDB servers/FOLDpro_TS1 name FOLDpro_TS1 ReadConformPDB servers/FOLDpro_TS2 name FOLDpro_TS2 ReadConformPDB servers/FOLDpro_TS3 name FOLDpro_TS3 ReadConformPDB servers/FOLDpro_TS4 name FOLDpro_TS4 ReadConformPDB servers/FOLDpro_TS5 name FOLDpro_TS5 ReadConformPDB servers/FUGUE_KM_AL1.pdb.gz name FUGUE_KM_AL1 ReadConformPDB servers/FUGUE_KM_AL2.pdb.gz name FUGUE_KM_AL2 ReadConformPDB servers/FUGUE_KM_AL3.pdb.gz name FUGUE_KM_AL3 ReadConformPDB servers/FUGUE_KM_AL4.pdb.gz name FUGUE_KM_AL4 ReadConformPDB servers/FUGUE_KM_AL5.pdb.gz name FUGUE_KM_AL5 ReadConformPDB servers/Fiser-M4T_TS1 name Fiser-M4T_TS1 ReadConformPDB servers/Frankenstein_TS1 name Frankenstein_TS1 ReadConformPDB servers/Frankenstein_TS2 name Frankenstein_TS2 ReadConformPDB servers/Frankenstein_TS3 name Frankenstein_TS3 ReadConformPDB servers/Frankenstein_TS4 name Frankenstein_TS4 ReadConformPDB servers/Frankenstein_TS5 name Frankenstein_TS5 ReadConformPDB servers/GS-KudlatyPred_TS1 name GS-KudlatyPred_TS1 ReadConformPDB servers/GS-MetaServer2_TS1 name GS-MetaServer2_TS1 ReadConformPDB servers/GS-MetaServer2_TS2 name GS-MetaServer2_TS2 ReadConformPDB servers/GS-MetaServer2_TS3 name GS-MetaServer2_TS3 ReadConformPDB servers/GS-MetaServer2_TS4 name GS-MetaServer2_TS4 ReadConformPDB servers/GS-MetaServer2_TS5 name GS-MetaServer2_TS5 ReadConformPDB servers/GeneSilicoMetaServer_TS1 name GeneSilicoMetaServer_TS1 ReadConformPDB servers/GeneSilicoMetaServer_TS2 name GeneSilicoMetaServer_TS2 ReadConformPDB servers/GeneSilicoMetaServer_TS3 name GeneSilicoMetaServer_TS3 ReadConformPDB servers/GeneSilicoMetaServer_TS4 name GeneSilicoMetaServer_TS4 ReadConformPDB servers/GeneSilicoMetaServer_TS5 name GeneSilicoMetaServer_TS5 ReadConformPDB servers/HHpred2_TS1 name HHpred2_TS1 ReadConformPDB servers/HHpred4_TS1 name HHpred4_TS1 ReadConformPDB servers/HHpred5_TS1 name HHpred5_TS1 ReadConformPDB servers/LOOPP_Server_TS1 name LOOPP_Server_TS1 ReadConformPDB servers/LOOPP_Server_TS2 name LOOPP_Server_TS2 ReadConformPDB servers/LOOPP_Server_TS3 name LOOPP_Server_TS3 ReadConformPDB servers/LOOPP_Server_TS4 name LOOPP_Server_TS4 ReadConformPDB servers/LOOPP_Server_TS5 name LOOPP_Server_TS5 ReadConformPDB servers/METATASSER_TS1 name METATASSER_TS1 ReadConformPDB servers/METATASSER_TS2 name METATASSER_TS2 ReadConformPDB servers/METATASSER_TS3 name METATASSER_TS3 ReadConformPDB servers/METATASSER_TS4 name METATASSER_TS4 ReadConformPDB servers/METATASSER_TS5 name METATASSER_TS5 ReadConformPDB servers/MUFOLD-MD_TS1 name MUFOLD-MD_TS1 ReadConformPDB servers/MUFOLD-MD_TS2 name MUFOLD-MD_TS2 ReadConformPDB servers/MUFOLD-MD_TS3 name MUFOLD-MD_TS3 ReadConformPDB servers/MUFOLD-MD_TS4 name MUFOLD-MD_TS4 ReadConformPDB servers/MUFOLD-MD_TS5 name MUFOLD-MD_TS5 ReadConformPDB servers/MUFOLD-Server_TS1 name MUFOLD-Server_TS1 ReadConformPDB servers/MUFOLD-Server_TS2 name MUFOLD-Server_TS2 ReadConformPDB servers/MUFOLD-Server_TS3 name MUFOLD-Server_TS3 ReadConformPDB servers/MUFOLD-Server_TS4 name MUFOLD-Server_TS4 ReadConformPDB servers/MUFOLD-Server_TS5 name MUFOLD-Server_TS5 ReadConformPDB servers/MULTICOM-CLUSTER_TS1 name MULTICOM-CLUSTER_TS1 ReadConformPDB servers/MULTICOM-CLUSTER_TS2 name MULTICOM-CLUSTER_TS2 ReadConformPDB servers/MULTICOM-CLUSTER_TS3 name MULTICOM-CLUSTER_TS3 ReadConformPDB servers/MULTICOM-CLUSTER_TS4 name MULTICOM-CLUSTER_TS4 ReadConformPDB servers/MULTICOM-CLUSTER_TS5 name MULTICOM-CLUSTER_TS5 ReadConformPDB servers/MULTICOM-CMFR_TS1 name MULTICOM-CMFR_TS1 ReadConformPDB servers/MULTICOM-CMFR_TS2 name MULTICOM-CMFR_TS2 ReadConformPDB servers/MULTICOM-CMFR_TS3 name MULTICOM-CMFR_TS3 ReadConformPDB servers/MULTICOM-CMFR_TS4 name MULTICOM-CMFR_TS4 ReadConformPDB servers/MULTICOM-CMFR_TS5 name MULTICOM-CMFR_TS5 ReadConformPDB servers/MULTICOM-RANK_TS1 name MULTICOM-RANK_TS1 ReadConformPDB servers/MULTICOM-RANK_TS2 name MULTICOM-RANK_TS2 ReadConformPDB servers/MULTICOM-RANK_TS3 name MULTICOM-RANK_TS3 ReadConformPDB servers/MULTICOM-RANK_TS4 name MULTICOM-RANK_TS4 ReadConformPDB servers/MULTICOM-RANK_TS5 name MULTICOM-RANK_TS5 ReadConformPDB servers/MULTICOM-REFINE_TS1 name MULTICOM-REFINE_TS1 ReadConformPDB servers/MULTICOM-REFINE_TS2 name MULTICOM-REFINE_TS2 ReadConformPDB servers/MULTICOM-REFINE_TS3 name MULTICOM-REFINE_TS3 ReadConformPDB servers/MULTICOM-REFINE_TS4 name MULTICOM-REFINE_TS4 ReadConformPDB servers/MULTICOM-REFINE_TS5 name MULTICOM-REFINE_TS5 ReadConformPDB servers/MUProt_TS1 name MUProt_TS1 ReadConformPDB servers/MUProt_TS2 name MUProt_TS2 ReadConformPDB servers/MUProt_TS3 name MUProt_TS3 ReadConformPDB servers/MUProt_TS4 name MUProt_TS4 ReadConformPDB servers/MUProt_TS5 name MUProt_TS5 ReadConformPDB servers/MUSTER_TS1 name MUSTER_TS1 ReadConformPDB servers/MUSTER_TS2 name MUSTER_TS2 ReadConformPDB servers/MUSTER_TS3 name MUSTER_TS3 ReadConformPDB servers/MUSTER_TS4 name MUSTER_TS4 ReadConformPDB servers/MUSTER_TS5 name MUSTER_TS5 ReadConformPDB servers/OLGAFS_TS1 name OLGAFS_TS1 ReadConformPDB servers/OLGAFS_TS2 name OLGAFS_TS2 ReadConformPDB servers/OLGAFS_TS3 name OLGAFS_TS3 ReadConformPDB servers/OLGAFS_TS4 name OLGAFS_TS4 ReadConformPDB servers/OLGAFS_TS5 name OLGAFS_TS5 ReadConformPDB servers/PS2-server_TS1 name PS2-server_TS1 ReadConformPDB servers/PS2-server_TS2 name PS2-server_TS2 ReadConformPDB servers/PS2-server_TS3 name PS2-server_TS3 ReadConformPDB servers/PS2-server_TS4 name PS2-server_TS4 ReadConformPDB servers/PS2-server_TS5 name PS2-server_TS5 ReadConformPDB servers/PSI_TS1 name PSI_TS1 ReadConformPDB servers/PSI_TS2 name PSI_TS2 ReadConformPDB servers/PSI_TS3 name PSI_TS3 ReadConformPDB servers/PSI_TS4 name PSI_TS4 ReadConformPDB servers/PSI_TS5 name PSI_TS5 ReadConformPDB servers/Pcons_dot_net_TS1 name Pcons_dot_net_TS1 ReadConformPDB servers/Pcons_dot_net_TS2 name Pcons_dot_net_TS2 ReadConformPDB servers/Pcons_dot_net_TS3 name Pcons_dot_net_TS3 ReadConformPDB servers/Pcons_dot_net_TS4 name Pcons_dot_net_TS4 ReadConformPDB servers/Pcons_dot_net_TS5 name Pcons_dot_net_TS5 ReadConformPDB servers/Pcons_local_TS1 name Pcons_local_TS1 ReadConformPDB servers/Pcons_local_TS2 name Pcons_local_TS2 ReadConformPDB servers/Pcons_local_TS3 name Pcons_local_TS3 ReadConformPDB servers/Pcons_local_TS4 name Pcons_local_TS4 ReadConformPDB servers/Pcons_local_TS5 name Pcons_local_TS5 ReadConformPDB servers/Pcons_multi_TS1 name Pcons_multi_TS1 ReadConformPDB servers/Pcons_multi_TS2 name Pcons_multi_TS2 ReadConformPDB servers/Pcons_multi_TS3 name Pcons_multi_TS3 ReadConformPDB servers/Pcons_multi_TS4 name Pcons_multi_TS4 ReadConformPDB servers/Pcons_multi_TS5 name Pcons_multi_TS5 ReadConformPDB servers/Phragment_TS1 name Phragment_TS1 ReadConformPDB servers/Phragment_TS2 name Phragment_TS2 ReadConformPDB servers/Phragment_TS3 name Phragment_TS3 ReadConformPDB servers/Phragment_TS4 name Phragment_TS4 ReadConformPDB servers/Phragment_TS5 name Phragment_TS5 ReadConformPDB servers/Phyre2_TS1 name Phyre2_TS1 ReadConformPDB servers/Phyre2_TS2 name Phyre2_TS2 ReadConformPDB servers/Phyre2_TS3 name Phyre2_TS3 ReadConformPDB servers/Phyre2_TS4 name Phyre2_TS4 ReadConformPDB servers/Phyre2_TS5 name Phyre2_TS5 ReadConformPDB servers/Phyre_de_novo_TS1 name Phyre_de_novo_TS1 ReadConformPDB servers/Phyre_de_novo_TS2 name Phyre_de_novo_TS2 ReadConformPDB servers/Phyre_de_novo_TS3 name Phyre_de_novo_TS3 ReadConformPDB servers/Phyre_de_novo_TS4 name Phyre_de_novo_TS4 ReadConformPDB servers/Phyre_de_novo_TS5 name Phyre_de_novo_TS5 ReadConformPDB servers/Poing_TS1 name Poing_TS1 ReadConformPDB servers/Poing_TS2 name Poing_TS2 ReadConformPDB servers/Poing_TS3 name Poing_TS3 ReadConformPDB servers/Poing_TS4 name Poing_TS4 ReadConformPDB servers/Poing_TS5 name Poing_TS5 ReadConformPDB servers/Pushchino_TS1 name Pushchino_TS1 ReadConformPDB servers/RAPTOR_TS1 name RAPTOR_TS1 ReadConformPDB servers/RAPTOR_TS2 name RAPTOR_TS2 ReadConformPDB servers/RAPTOR_TS3 name RAPTOR_TS3 ReadConformPDB servers/RAPTOR_TS4 name RAPTOR_TS4 ReadConformPDB servers/RBO-Proteus_TS1 name RBO-Proteus_TS1 ReadConformPDB servers/RBO-Proteus_TS2 name RBO-Proteus_TS2 ReadConformPDB servers/RBO-Proteus_TS3 name RBO-Proteus_TS3 ReadConformPDB servers/RBO-Proteus_TS4 name RBO-Proteus_TS4 ReadConformPDB servers/RBO-Proteus_TS5 name RBO-Proteus_TS5 # ReadConformPDB servers/SAM-T02-server_AL1.pdb.gz name SAM-T02-server_AL1 # ReadConformPDB servers/SAM-T02-server_AL2.pdb.gz name SAM-T02-server_AL2 # ReadConformPDB servers/SAM-T02-server_AL3.pdb.gz name SAM-T02-server_AL3 # ReadConformPDB servers/SAM-T02-server_AL4.pdb.gz name SAM-T02-server_AL4 # ReadConformPDB servers/SAM-T02-server_AL5.pdb.gz name SAM-T02-server_AL5 # ReadConformPDB servers/SAM-T06-server_TS1 name SAM-T06-server_TS1 # ReadConformPDB servers/SAM-T06-server_TS2 name SAM-T06-server_TS2 # ReadConformPDB servers/SAM-T06-server_TS3 name SAM-T06-server_TS3 # ReadConformPDB servers/SAM-T06-server_TS4 name SAM-T06-server_TS4 # ReadConformPDB servers/SAM-T06-server_TS5 name SAM-T06-server_TS5 # ReadConformPDB servers/SAM-T08-server_TS1 name SAM-T08-server_TS1 # ReadConformPDB servers/SAM-T08-server_TS2 name SAM-T08-server_TS2 # ReadConformPDB servers/SAM-T08-server_TS3 name SAM-T08-server_TS3 # ReadConformPDB servers/SAM-T08-server_TS4 name SAM-T08-server_TS4 # ReadConformPDB servers/SAM-T08-server_TS5 name SAM-T08-server_TS5 ReadConformPDB servers/YASARA_TS1 name YASARA_TS1 ReadConformPDB servers/YASARA_TS2 name YASARA_TS2 ReadConformPDB servers/YASARA_TS3 name YASARA_TS3 ReadConformPDB servers/YASARA_TS4 name YASARA_TS4 ReadConformPDB servers/YASARA_TS5 name YASARA_TS5 ReadConformPDB servers/Zhang-Server_TS1 name Zhang-Server_TS1 ReadConformPDB servers/Zhang-Server_TS2 name Zhang-Server_TS2 ReadConformPDB servers/Zhang-Server_TS3 name Zhang-Server_TS3 ReadConformPDB servers/Zhang-Server_TS4 name Zhang-Server_TS4 ReadConformPDB servers/Zhang-Server_TS5 name Zhang-Server_TS5 ReadConformPDB servers/circle_TS1 name circle_TS1 ReadConformPDB servers/circle_TS2 name circle_TS2 ReadConformPDB servers/circle_TS3 name circle_TS3 ReadConformPDB servers/circle_TS4 name circle_TS4 ReadConformPDB servers/circle_TS5 name circle_TS5 ReadConformPDB servers/forecast_TS1 name forecast_TS1 ReadConformPDB servers/forecast_TS2 name forecast_TS2 ReadConformPDB servers/forecast_TS3 name forecast_TS3 ReadConformPDB servers/forecast_TS4 name forecast_TS4 ReadConformPDB servers/forecast_TS5 name forecast_TS5 ReadConformPDB servers/huber-torda-server_TS1 name huber-torda-server_TS1 ReadConformPDB servers/huber-torda-server_TS2 name huber-torda-server_TS2 ReadConformPDB servers/huber-torda-server_TS3 name huber-torda-server_TS3 ReadConformPDB servers/huber-torda-server_TS4 name huber-torda-server_TS4 ReadConformPDB servers/huber-torda-server_TS5 name huber-torda-server_TS5 ReadConformPDB servers/keasar-server_TS1 name keasar-server_TS1 ReadConformPDB servers/keasar-server_TS2 name keasar-server_TS2 ReadConformPDB servers/keasar-server_TS3 name keasar-server_TS3 ReadConformPDB servers/keasar-server_TS4 name keasar-server_TS4 ReadConformPDB servers/keasar-server_TS5 name keasar-server_TS5 ReadConformPDB servers/mGenTHREADER_TS1 name mGenTHREADER_TS1 ReadConformPDB servers/mahmood-torda-server_TS1 name mahmood-torda-server_TS1 ReadConformPDB servers/mahmood-torda-server_TS2 name mahmood-torda-server_TS2 ReadConformPDB servers/mahmood-torda-server_TS3 name mahmood-torda-server_TS3 ReadConformPDB servers/mahmood-torda-server_TS4 name mahmood-torda-server_TS4 ReadConformPDB servers/mahmood-torda-server_TS5 name mahmood-torda-server_TS5 ReadConformPDB servers/mariner1_TS1 name mariner1_TS1 ReadConformPDB servers/mariner1_TS2 name mariner1_TS2 ReadConformPDB servers/mariner1_TS3 name mariner1_TS3 ReadConformPDB servers/mariner1_TS4 name mariner1_TS4 ReadConformPDB servers/mariner1_TS5 name mariner1_TS5 ReadConformPDB servers/nFOLD3_TS1 name nFOLD3_TS1 ReadConformPDB servers/nFOLD3_TS2 name nFOLD3_TS2 ReadConformPDB servers/nFOLD3_TS3 name nFOLD3_TS3 ReadConformPDB servers/nFOLD3_TS4 name nFOLD3_TS4 ReadConformPDB servers/nFOLD3_TS5 name nFOLD3_TS5 ReadConformPDB servers/panther_server_TS2 name panther_server_TS2 ReadConformPDB servers/panther_server_TS3 name panther_server_TS3 ReadConformPDB servers/panther_server_TS4 name panther_server_TS4 ReadConformPDB servers/panther_server_TS5 name panther_server_TS5 ReadConformPDB servers/pipe_int_TS1 name pipe_int_TS1 ReadConformPDB servers/pipe_int_TS2 name pipe_int_TS2 ReadConformPDB servers/pipe_int_TS3 name pipe_int_TS3 ReadConformPDB servers/pipe_int_TS4 name pipe_int_TS4 ReadConformPDB servers/pipe_int_TS5 name pipe_int_TS5 ReadConformPDB servers/pro-sp3-TASSER_TS1 name pro-sp3-TASSER_TS1 ReadConformPDB servers/pro-sp3-TASSER_TS2 name pro-sp3-TASSER_TS2 ReadConformPDB servers/pro-sp3-TASSER_TS3 name pro-sp3-TASSER_TS3 ReadConformPDB servers/pro-sp3-TASSER_TS4 name pro-sp3-TASSER_TS4 ReadConformPDB servers/pro-sp3-TASSER_TS5 name pro-sp3-TASSER_TS5 ReadConformPDB servers/rehtnap_TS1 name rehtnap_TS1 ReadConformPDB servers/rehtnap_TS2 name rehtnap_TS2 ReadConformPDB servers/rehtnap_TS3 name rehtnap_TS3 ReadConformPDB servers/schenk-torda-server_TS1 name schenk-torda-server_TS1 ReadConformPDB servers/schenk-torda-server_TS2 name schenk-torda-server_TS2 ReadConformPDB servers/schenk-torda-server_TS3 name schenk-torda-server_TS3 ReadConformPDB servers/schenk-torda-server_TS4 name schenk-torda-server_TS4 ReadConformPDB servers/schenk-torda-server_TS5 name schenk-torda-server_TS5 InFilePrefix OutFilePrefix decoys/ InitMethodProbs \ Backrub 0.5 \ BigBackrub 0.3 \ FixOmega 0.3 \ 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 0 \ InsertSpecificFragment 0 \ InsertFragment 5 \ TwoFragment 5 \ CrossOver 15 \ DoubleCross 15 \ CrossAndInsert 15 \ ReduceClash 5 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0498.MQAX4-opt1 PrintConformPDB T0498.MQAX4-opt1.pdb CostConform Time // Edit this to include full sets of alignments from any // strongly-predicted superfamily // InfilePrefix 1xxxX/ // include read-alignments-scwrl.under Include T0498.t04.undertaker-align.under Include T0498.t06.undertaker-align.under Include T0498.t2k.undertaker-align.under Include T0498.undertaker-align.under # SCWRL can take a while, so decide whether or not to use it based on # time available. # ReadFragmentAlignment NOFILTER SCWRL force_alignment all-align.a2m ReadFragmentAlignment NOFILTER force_alignment all-align.a2m InfilePrefix Time # ReportCost MQAX4.rdb InitMethodProbs \ Backrub 2 \ BigBackrub 1 \ FixOmega 1 \ OneRotamer 5 \ ClashingRotamer 1 \ ClusteredRotamer 1 \ CrossOver 5 \ DoubleCross 5 \ 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 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0498.MQAX4-opt1 PrintConformPDB T0498.MQAX4-opt1.pdb SCWRLConform NameConform T0498.MQAX4-opt1-scwrl PrintConformPDB T0498.MQAX4-opt1-scwrl.pdb CostConform Time ScaleCost break 2 soft_clashes 2 CostConform Time InitMethodProbs \ Backrub 2 \ BigBackrub 1 \ FixOmega 1 \ 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 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0498.MQAX4-opt2 PrintConformPDB T0498.MQAX4-opt2.pdb CostConform ScaleCost break 2 soft_clashes 2 CostConform Time OptConform pool_size 40 num_gen 60 gen_size 100 \ super_iter 2 super_num_gen 300 use_all NameConform T0498.MQAX4-opt3 PrintConformPDB T0498.MQAX4-opt3.pdb # PrintConformHbonds MQAX4-opt3.all-hbonds # PrintConformHbonds nonhelix backbone MQAX4-opt3.beta-hbonds PrintConformSheets MQAX4-opt3.sheets PrintConformHelices MQAX4-opt3.helices PrintConstraints all MQAX4-opt3.constraints # PrintConformBreaks MQAX4-opt3.breaks CostConform Time quit