id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9483 No error message when timeout exceeded jheld@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Trying to run a simple modeller comparative job. Log is below. I can't run any Modeller comp jobs with the webserver for the last several days. modeller comparative ""bp7 [3]:1"" numModels 2 fast true multichain true hetPreserve false hydrogens false waterPreserve false directory /Users/jasonheld/DesktopWebservices job id: OHN550A7YYFEN7XX 2023-07-30 14:56:13,169 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 60] Operation timed out')': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/status Modeller job (ID V2AT7AYF0IV6EV9J) finished Modeller failure with no error output Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ""Blast Protein"" > blastprotein > MARPFTLIVLLSAHLCLHVVVTQDEDSHINTQLLSSVLDRLTNRTTYDKRLRPRYGEKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFIRQSQIQEEQRNSQIL > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 300 version None name bp1 Webservices job id: OOC72OMB6QZH09EM > ui tool show ""Blast Protein"" > blastprotein > MARPFTLIVLLSAHLCLHVVVTQDEDSHINTQLLSSVLDRLTNRTTYDKRLRPRYGEKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFIRQSQIQEEQRNSQIL > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 500 version None name bp2 Webservices job id: 7RV4QK2WBVYL0HM4 > ui tool show ""Blast Protein"" > blastprotein > MARPFTLIVLLSAHLCLHVVVTQDEDSHINTQLLSSVLDRLTNRTTYDKRLRPRYGEKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFIRQSQIQEEQRNSQIL > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 1000 version None name bp3 Webservices job id: WFXX9Y9RC83M6247 > ui tool show ""Blast Protein"" > blastprotein > MARPFTLIVLLSAHLCLHVVVTQDEDSHINTQLLSSVLDRLTNRTTYDKRLRPRYGEKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFIRQSQIQEEQRNSQIL > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 300 version None name bp4 Webservices job id: XTSHHO229JC1ID4K Alignment identifier is bp4 [1] Showing conservation header (""seq_conservation"" residue attribute) for alignment bp4 [1] > sequence align ""bp4 [1]"" program clustalOmega replace true Webservices job id: 9Z53G8F2FIXPF3UY > ui tool show ""Modeller Comparative"" > modeller comparative ""bp4 [1]:1"" numModels 5 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop Alignment bp4 [1] has no associated chains Alignment identifier is bp4 [2] Showing conservation header (""seq_conservation"" residue attribute) for alignment bp4 [2] > sequence align ""bp4 [2]"" program clustalOmega replace true Webservices job id: FDLKICRJ3ZLOQ3H5 > ui tool show ""Modeller Comparative"" > modeller comparative ""bp4 [2]:1"" numModels 5 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop Alignment bp4 [2] has no associated chains Alignment identifier is bp4 [3] Showing conservation header (""seq_conservation"" residue attribute) for alignment bp4 [3] > sequence align ""bp4 [3]"" program clustalOmega replace true Webservices job id: ZQRX2TW89TO3SQAT > ui tool show ""Modeller Comparative"" > modeller comparative ""bp4 [3]:1"" numModels 5 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop Alignment bp4 [3] has no associated chains > save /Users/jasonheld/Desktop/pir format pir alignment ""bp4 [3]"" > modeller comparative ""bp4 [3]:1"" numModels 5 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop Alignment bp4 [3] has no associated chains > open /Users/jasonheld/Desktop/pir Failed opening file /Users/jasonheld/Desktop/pir: '/Users/jasonheld/Desktop/pir' has no suffix > open /Users/jasonheld/Desktop/pir '/Users/jasonheld/Desktop/pir' has no suffix > open /Users/jasonheld/Desktop/pir.pir Summary of feedback from opening /Users/jasonheld/Desktop/pir.pir --- notes | Alignment identifier is pir.pir Showing conservation header (""seq_conservation"" residue attribute) for alignment pir.pir Opened 46 sequences from pir.pir > modeller comparative pir.pir:1 numModels 5 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop Alignment pir.pir has no associated chains Alignment identifier is bp4 [4] Showing conservation header (""seq_conservation"" residue attribute) for alignment bp4 [4] > ui tool show ""Modeller Comparative"" > modeller comparative ""bp4 [4]:1"" numModels 5 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop Alignment bp4 [4] has no associated chains > ui tool show ""Blast Protein"" > open > /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/SWISSMODEL/G5EBQ0UNC49B_LT_SQPARAA_ModelledOn6PXD/model/model_6PXD.pdb model_6PXD.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) G5EBQ0|UNC49B_LT_SQPARAA [more info...] Chain information for model_6PXD.pdb #1 --- Chain | Description A B C D E | No description available > close > blastprotein > MARPFTLIVLLSAHLCLHVVVTQDEDSHINTQLLSSVLDRLTNRTTYDKRLRPRYGEKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFIRQSQIQEEQRNSQIL > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp5 Webservices job id: YIP0OOU3KNBPWR8W > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #1 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #2 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #3 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #4 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #5 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear Alignment identifier is bp5 [1] Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment bp5 [1] > ui tool show ""Modeller Comparative"" > modeller comparative ""bp5 [1]:1"" numModels 1 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop > close #1-5 > ui tool show ""Blast Protein"" > blastprotein > MARPFTLIVLLSAHLCLHVVVTQDEDSHINTQLLSSVLDRLTNRTTYDKRLRPRYGEKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFIRQSQIQEEQRNSQIL > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 300 version None name bp6 Webservices job id: D8LI5JJXTX9B8PM9 Webservices job id: V2AT7AYF0IV6EV9J > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #1 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #2 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #3 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #4 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:4NPQ Summary of feedback from opening 4NPQ fetched from pdb --- warnings | Atom O has no neighbors to form bonds with according to residue template for ARG /E:138 Atom NZ has no neighbors to form bonds with according to residue template for LYS /P:38 4npq title: The resting-state conformation of the GLIC ligand-gated ion channel [more info...] Chain information for 4npq #5 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T | Proton-gated ion channel | GLIC_GLOVI 2-317 4npq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select clear > open pdb:6BE1 Summary of feedback from opening 6BE1 fetched from pdb --- notes | Fetching compressed mmCIF 6be1 from http://files.rcsb.org/download/6be1.cif Fetching CCD NA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif 6be1 title: Cryo-EM structure of serotonin receptor [more info...] Chain information for 6be1 #6 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | E9QLC0_MOUSE 6-462 Non-standard residues in 6be1 #6 --- BMA — beta-D-mannopyranose CL — chloride ion NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6BE1 6be1 title: Cryo-EM structure of serotonin receptor [more info...] Chain information for 6be1 #7 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | E9QLC0_MOUSE 6-462 Non-standard residues in 6be1 #7 --- BMA — beta-D-mannopyranose CL — chloride ion NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6BE1 6be1 title: Cryo-EM structure of serotonin receptor [more info...] Chain information for 6be1 #8 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | E9QLC0_MOUSE 6-462 Non-standard residues in 6be1 #8 --- BMA — beta-D-mannopyranose CL — chloride ion NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6BE1 6be1 title: Cryo-EM structure of serotonin receptor [more info...] Chain information for 6be1 #9 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | E9QLC0_MOUSE 6-462 Non-standard residues in 6be1 #9 --- BMA — beta-D-mannopyranose CL — chloride ion NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6BE1 6be1 title: Cryo-EM structure of serotonin receptor [more info...] Chain information for 6be1 #10 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | E9QLC0_MOUSE 6-462 Non-standard residues in 6be1 #10 --- BMA — beta-D-mannopyranose CL — chloride ion NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6HIS Summary of feedback from opening 6HIS fetched from pdb --- notes | Fetching compressed mmCIF 6his from http://files.rcsb.org/download/6his.cif Fetching CCD TKT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/TKT/TKT.cif 6his title: Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation [more info...] Chain information for 6his #11 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | 5HT3A_MOUSE 8-458 Non-standard residues in 6his #11 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) TKT — (3-ENDO)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate (tropisetron) > select clear > open pdb:6HIS 6his title: Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation [more info...] Chain information for 6his #12 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | 5HT3A_MOUSE 8-458 Non-standard residues in 6his #12 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) TKT — (3-ENDO)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate (tropisetron) > select clear > open pdb:6HIS 6his title: Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation [more info...] Chain information for 6his #13 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | 5HT3A_MOUSE 8-458 Non-standard residues in 6his #13 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) TKT — (3-ENDO)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate (tropisetron) > select clear > open pdb:6HIS 6his title: Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation [more info...] Chain information for 6his #14 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | 5HT3A_MOUSE 8-458 Non-standard residues in 6his #14 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) TKT — (3-ENDO)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate (tropisetron) > select clear > open pdb:6HIS 6his title: Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation [more info...] Chain information for 6his #15 --- Chain | Description | UniProt A B C D E | 5-hydroxytryptamine receptor 3A | 5HT3A_MOUSE 8-458 Non-standard residues in 6his #15 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) TKT — (3-ENDO)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate (tropisetron) > select clear > open pdb:6HUG 6hug title: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. [more info...] Chain information for 6hug #16 --- Chain | Description | UniProt A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_BOVIN 1-429 B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN -24-448 C | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN -38-436 G | Megabody Mb38 | Non-standard residues in 6hug #16 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) RI5 — (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione (picrotoxin) > select clear > open pdb:6HUG 6hug title: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. [more info...] Chain information for 6hug #17 --- Chain | Description | UniProt A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_BOVIN 1-429 B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN -24-448 C | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN -38-436 G | Megabody Mb38 | Non-standard residues in 6hug #17 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) RI5 — (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione (picrotoxin) > select clear > open pdb:6HUG 6hug title: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. [more info...] Chain information for 6hug #18 --- Chain | Description | UniProt A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_BOVIN 1-429 B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN -24-448 C | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN -38-436 G | Megabody Mb38 | Non-standard residues in 6hug #18 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) RI5 — (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione (picrotoxin) > select clear > open pdb:6HUG 6hug title: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. [more info...] Chain information for 6hug #19 --- Chain | Description | UniProt A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_BOVIN 1-429 B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN -24-448 C | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN -38-436 G | Megabody Mb38 | Non-standard residues in 6hug #19 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) RI5 — (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione (picrotoxin) > select clear > open pdb:6HUG 6hug title: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. [more info...] Chain information for 6hug #20 --- Chain | Description | UniProt A D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_BOVIN 1-429 B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN -24-448 C | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN -38-436 G | Megabody Mb38 | Non-standard residues in 6hug #20 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) RI5 — (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione (picrotoxin) > select clear > open pdb:6PXD 6pxd title: CryoEM structure of zebra fish alpha-1 glycine receptor, Apo state [more info...] Chain information for 6pxd #21 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-325 329-362 Non-standard residues in 6pxd #21 --- CL — chloride ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select clear > open pdb:6PXD 6pxd title: CryoEM structure of zebra fish alpha-1 glycine receptor, Apo state [more info...] Chain information for 6pxd #22 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-325 329-362 Non-standard residues in 6pxd #22 --- CL — chloride ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select clear > open pdb:6PXD 6pxd title: CryoEM structure of zebra fish alpha-1 glycine receptor, Apo state [more info...] Chain information for 6pxd #23 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-325 329-362 Non-standard residues in 6pxd #23 --- CL — chloride ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select clear > open pdb:6PXD 6pxd title: CryoEM structure of zebra fish alpha-1 glycine receptor, Apo state [more info...] Chain information for 6pxd #24 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-325 329-362 Non-standard residues in 6pxd #24 --- CL — chloride ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select clear > open pdb:6PXD 6pxd title: CryoEM structure of zebra fish alpha-1 glycine receptor, Apo state [more info...] Chain information for 6pxd #25 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-325 329-362 Non-standard residues in 6pxd #25 --- CL — chloride ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select clear > open pdb:6UBS 6ubs title: Full length Glycine receptor reconstituted in lipid nanodisc in Apo/Resting conformation [more info...] Chain information for 6ubs #26 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE 1-444 Non-standard residues in 6ubs #26 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6UBS 6ubs title: Full length Glycine receptor reconstituted in lipid nanodisc in Apo/Resting conformation [more info...] Chain information for 6ubs #27 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE 1-444 Non-standard residues in 6ubs #27 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6UBS 6ubs title: Full length Glycine receptor reconstituted in lipid nanodisc in Apo/Resting conformation [more info...] Chain information for 6ubs #28 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE 1-444 Non-standard residues in 6ubs #28 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6UBS 6ubs title: Full length Glycine receptor reconstituted in lipid nanodisc in Apo/Resting conformation [more info...] Chain information for 6ubs #29 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE 1-444 Non-standard residues in 6ubs #29 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6UBS 6ubs title: Full length Glycine receptor reconstituted in lipid nanodisc in Apo/Resting conformation [more info...] Chain information for 6ubs #30 --- Chain | Description | UniProt A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE 1-444 Non-standard residues in 6ubs #30 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine > select clear > open pdb:6UWZ Summary of feedback from opening 6UWZ fetched from pdb --- notes | Fetching compressed mmCIF 6uwz from http://files.rcsb.org/download/6uwz.cif Fetching CCD P1L from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/P1L/P1L.cif Fetching CCD POV from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/POV/POV.cif Fetching CCD OCT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/OCT/OCT.cif 6uwz title: Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha- bungarotoxin [more info...] Chain information for 6uwz #31 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 F G | Alpha-bungarotoxin | 3L21A_BUNMU 1-74 Non-standard residues in 6uwz #31 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose OCT — N-octane POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:6UWZ 6uwz title: Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha- bungarotoxin [more info...] Chain information for 6uwz #32 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 F G | Alpha-bungarotoxin | 3L21A_BUNMU 1-74 Non-standard residues in 6uwz #32 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose OCT — N-octane POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:6UWZ 6uwz title: Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha- bungarotoxin [more info...] Chain information for 6uwz #33 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 F G | Alpha-bungarotoxin | 3L21A_BUNMU 1-74 Non-standard residues in 6uwz #33 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose OCT — N-octane POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:6UWZ 6uwz title: Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha- bungarotoxin [more info...] Chain information for 6uwz #34 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 F G | Alpha-bungarotoxin | 3L21A_BUNMU 1-74 Non-standard residues in 6uwz #34 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose OCT — N-octane POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:6UWZ 6uwz title: Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha- bungarotoxin [more info...] Chain information for 6uwz #35 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 F G | Alpha-bungarotoxin | 3L21A_BUNMU 1-74 Non-standard residues in 6uwz #35 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose OCT — N-octane POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:6ZGD 6zgd title: GLIC pentameric ligand-gated ion channel, pH 7 [more info...] Chain information for 6zgd #36 --- Chain | Description | UniProt A B C D E | Proton-gated ion channel | GLIC_GLOVI 2-317 > select clear > open pdb:6ZGD 6zgd title: GLIC pentameric ligand-gated ion channel, pH 7 [more info...] Chain information for 6zgd #37 --- Chain | Description | UniProt A B C D E | Proton-gated ion channel | GLIC_GLOVI 2-317 > select clear > open pdb:6ZGD 6zgd title: GLIC pentameric ligand-gated ion channel, pH 7 [more info...] Chain information for 6zgd #38 --- Chain | Description | UniProt A B C D E | Proton-gated ion channel | GLIC_GLOVI 2-317 > select clear > open pdb:6ZGD 6zgd title: GLIC pentameric ligand-gated ion channel, pH 7 [more info...] Chain information for 6zgd #39 --- Chain | Description | UniProt A B C D E | Proton-gated ion channel | GLIC_GLOVI 2-317 > select clear > open pdb:6ZGD 6zgd title: GLIC pentameric ligand-gated ion channel, pH 7 [more info...] Chain information for 6zgd #40 --- Chain | Description | UniProt A B C D E | Proton-gated ion channel | GLIC_GLOVI 2-317 > select clear > open pdb:7SMM Summary of feedback from opening 7SMM fetched from pdb --- notes | Fetching compressed mmCIF 7smm from http://files.rcsb.org/download/7smm.cif Fetching CCD CLR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/CLR/CLR.cif Fetching CCD DD9 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/DD9/DD9.cif 7smm title: Cryo-EM structure of Torpedo acetylcholine receptor in apo form [more info...] Chain information for 7smm #41 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 Non-standard residues in 7smm #41 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CLR — cholesterol DD9 — nonane MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:7SMM 7smm title: Cryo-EM structure of Torpedo acetylcholine receptor in apo form [more info...] Chain information for 7smm #42 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 Non-standard residues in 7smm #42 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CLR — cholesterol DD9 — nonane MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:7SMM 7smm title: Cryo-EM structure of Torpedo acetylcholine receptor in apo form [more info...] Chain information for 7smm #43 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 Non-standard residues in 7smm #43 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CLR — cholesterol DD9 — nonane MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:7SMM 7smm title: Cryo-EM structure of Torpedo acetylcholine receptor in apo form [more info...] Chain information for 7smm #44 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 Non-standard residues in 7smm #44 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CLR — cholesterol DD9 — nonane MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear > open pdb:7SMM 7smm title: Cryo-EM structure of Torpedo acetylcholine receptor in apo form [more info...] Chain information for 7smm #45 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 C | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 Non-standard residues in 7smm #45 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CLR — cholesterol DD9 — nonane MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > select clear Alignment identifier is bp6 [1] Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6ubs chain A to 6UBS_E with 0 mismatches Associated 6ubs chain B to 6UBS_E with 0 mismatches Associated 6ubs chain C to 6UBS_E with 0 mismatches Associated 6ubs chain D to 6UBS_E with 0 mismatches Associated 6ubs chain E to 6UBS_E with 0 mismatches Associated 6ubs chain A to 6UBS_E with 0 mismatches Associated 6ubs chain B to 6UBS_E with 0 mismatches Associated 6ubs chain C to 6UBS_E with 0 mismatches Associated 6ubs chain D to 6UBS_E with 0 mismatches Associated 6ubs chain E to 6UBS_E with 0 mismatches Associated 6ubs chain A to 6UBS_E with 0 mismatches Associated 6ubs chain B to 6UBS_E with 0 mismatches Associated 6ubs chain C to 6UBS_E with 0 mismatches Associated 6ubs chain D to 6UBS_E with 0 mismatches Associated 6ubs chain E to 6UBS_E with 0 mismatches Associated 6ubs chain A to 6UBS_E with 0 mismatches Associated 6ubs chain B to 6UBS_E with 0 mismatches Associated 6ubs chain C to 6UBS_E with 0 mismatches Associated 6ubs chain D to 6UBS_E with 0 mismatches Associated 6ubs chain E to 6UBS_E with 0 mismatches Associated 6ubs chain A to 6UBS_E with 0 mismatches Associated 6ubs chain B to 6UBS_E with 0 mismatches Associated 6ubs chain C to 6UBS_E with 0 mismatches Associated 6ubs chain D to 6UBS_E with 0 mismatches Associated 6ubs chain E to 6UBS_E with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment bp6 [1] > sequence align ""bp6 [1]"" program clustalOmega replace true Webservices job id: 2Y6CP0TICSYGAQP1 > ui tool show ""Modeller Comparative"" > modeller comparative ""bp6 [1]:1"" numModels 2 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop > save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX- > ModellerComparative/ChimeraX_Modeller_01.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 299, in process return copy_state(data, convert=convert) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 219, in copy_state return _copy(data) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 217, in _copy return convert(data) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 298, in convert return add_obj(obj, parents) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 142, in from_obj if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 476, in get_class return f(class_name) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/modeller/__init__.py"", line 27, in get_class return getattr(comparative, class_name) AttributeError: module 'chimerax.modeller.comparative' has no attribute 'ModellerWebJob' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> : module 'chimerax.modeller.comparative' has no attribute 'ModellerWebJob' ValueError: error processing: 'tasks' -> : module 'chimerax.modeller.comparative' has no attribute 'ModellerWebJob' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 299, in process return copy_state(data, convert=convert) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 219, in copy_state return _copy(data) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 204, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/state.py"", line 217, in _copy return convert(data) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 298, in convert return add_obj(obj, parents) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 142, in from_obj if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 476, in get_class return f(class_name) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/modeller/__init__.py"", line 27, in get_class return getattr(comparative, class_name) AttributeError: module 'chimerax.modeller.comparative' has no attribute 'ModellerWebJob' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> : module 'chimerax.modeller.comparative' has no attribute 'ModellerWebJob' ValueError: error processing: 'tasks' -> : module 'chimerax.modeller.comparative' has no attribute 'ModellerWebJob' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > hide #1.1 models > show #1.1 models Webservices job id: AN4ZDIPBXTZ47A8R > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!13 models > hide #!12 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!20 models > hide #21 models > hide #22 models > hide #23 models > hide #24 models > hide #25 models > hide #!26 models > hide #!27 models > hide #!28 models > hide #!29 models > hide #!30 models > hide #!31 models > hide #!32 models > hide #!33 models > hide #!34 models > hide #!35 models > hide #!36 models > hide #!37 models > hide #!38 models > hide #!39 models > hide #!40 models > hide #!41 models > hide #!42 models > hide #!43 models > hide #!44 models > hide #!45 models > hide #1.1 models > show #1.1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #1.1 models > ui tool show ""Modeller Comparative"" > ui tool show ""Blast Protein"" [Repeated 1 time(s)] > blastprotein > MARPFTLIVLLSAHLCLHVVVTQDEDSHINTQLLSSVLDRLTNRTTYDKRLRPRYGEKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFIRQSQIQEEQRNSQIL > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 300 version None name bp7 Webservices job id: ZV3NW05P67L09FDE Alignment identifier is bp7 [1] Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6be1 chain A to 6HIS_E with 0 mismatches Associated 6be1 chain B to 6HIS_E with 0 mismatches Associated 6be1 chain C to 6HIS_E with 0 mismatches Associated 6be1 chain D to 6HIS_E with 0 mismatches Associated 6be1 chain E to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6his chain A to 6HIS_E with 0 mismatches Associated 6his chain E to 6HIS_E with 0 mismatches Associated 6his chain B to 6HIS_E with 0 mismatches Associated 6his chain C to 6HIS_E with 0 mismatches Associated 6his chain D to 6HIS_E with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6hug chain C to 6HUG_C with 0 mismatches Associated 6hug chain B to 6HUG_E with 0 mismatches Associated 6hug chain E to 6HUG_E with 0 mismatches Associated 6hug chain A to 6HUG_D with 0 mismatches Associated 6hug chain D to 6HUG_D with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6pxd chain E to 6PXD_E with 0 mismatches Associated 6pxd chain A to 6PXD_E with 0 mismatches Associated 6pxd chain B to 6PXD_E with 0 mismatches Associated 6pxd chain C to 6PXD_E with 0 mismatches Associated 6pxd chain D to 6PXD_E with 0 mismatches Associated 6ubs chain A to 6UBS_B with 0 mismatches Associated 6ubs chain B to 6UBS_B with 0 mismatches Associated 6ubs chain C to 6UBS_B with 0 mismatches Associated 6ubs chain D to 6UBS_B with 0 mismatches Associated 6ubs chain E to 6UBS_B with 0 mismatches Associated 6ubs chain A to 6UBS_B with 0 mismatches Associated 6ubs chain B to 6UBS_B with 0 mismatches Associated 6ubs chain C to 6UBS_B with 0 mismatches Associated 6ubs chain D to 6UBS_B with 0 mismatches Associated 6ubs chain E to 6UBS_B with 0 mismatches Associated 6ubs chain A to 6UBS_B with 0 mismatches Associated 6ubs chain B to 6UBS_B with 0 mismatches Associated 6ubs chain C to 6UBS_B with 0 mismatches Associated 6ubs chain D to 6UBS_B with 0 mismatches Associated 6ubs chain E to 6UBS_B with 0 mismatches Associated 6ubs chain A to 6UBS_B with 0 mismatches Associated 6ubs chain B to 6UBS_B with 0 mismatches Associated 6ubs chain C to 6UBS_B with 0 mismatches Associated 6ubs chain D to 6UBS_B with 0 mismatches Associated 6ubs chain E to 6UBS_B with 0 mismatches Associated 6ubs chain A to 6UBS_B with 0 mismatches Associated 6ubs chain B to 6UBS_B with 0 mismatches Associated 6ubs chain C to 6UBS_B with 0 mismatches Associated 6ubs chain D to 6UBS_B with 0 mismatches Associated 6ubs chain E to 6UBS_B with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6uwz chain B to 7SMM_B with 0 mismatches Associated 6uwz chain E to 7SMM_E with 0 mismatches Associated 6uwz chain C to 7SMM_C with 0 mismatches Associated 6uwz chain A to 7SMM_D with 0 mismatches Associated 6uwz chain D to 7SMM_D with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Associated 7smm chain B to 7SMM_B with 0 mismatches Associated 7smm chain E to 7SMM_E with 0 mismatches Associated 7smm chain C to 7SMM_C with 0 mismatches Associated 7smm chain A to 7SMM_D with 0 mismatches Associated 7smm chain D to 7SMM_D with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment bp7 [1] > sequence align ""bp7 [1]"" program clustalOmega replace true Webservices job id: THV6Y43QTOHBS1YD > ui tool show ""Modeller Comparative"" > modeller comparative ""bp7 [1]:1"" numModels 2 fast false multichain true > hetPreserve false hydrogens false waterPreserve false executableLocation > /Library/modeller-10.4/py2_compat/mod10.4_mac10v4 directory > /Users/jasonheld/Desktop Modeller output FATAL ERROR: MODINSTALL10v4 environment variable not set: incomplete MODELLER installation Modeller errors Exception in thread Thread-1590: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/modeller/common.py"", line 692, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py"", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Library/modeller-10.4/py2_compat/mod10.4_mac10v4', '/Users/jasonheld/Desktop/ModellerModelling.py']' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973, in _bootstrap_inner self.run() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910, in run self._target(*self._args, **self._kwargs) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/modeller/common.py"", line 704, in threaded_run raise UserError(""Modeller execution failed; output and errors in log"") chimerax.core.errors.UserError: Modeller execution failed; output and errors in log > ui tool show ""Modeller Comparative"" > modeller comparative ""bp7 [1]:1"" numModels 2 fast false multichain true > hetPreserve false hydrogens false waterPreserve false executableLocation > /Users/jasonheld/miniconda3/lib/modeller-10.4/bin/mod10.4_mac10v4 directory > /Users/jasonheld/Desktop Modeller output Modeller errors dyld[96965]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.6/Python Referenced from: /Users/jasonheld/miniconda3/lib/modeller-10.4/bin/mod10.4_mac10v4 Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.6/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.6/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.6/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.6/Python' (no such file) Exception in thread Thread-1674: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/modeller/common.py"", line 692, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py"", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Users/jasonheld/miniconda3/lib/modeller-10.4/bin/mod10.4_mac10v4', '/Users/jasonheld/Desktop/ModellerModelling.py']' died with . During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973, in _bootstrap_inner self.run() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910, in run self._target(*self._args, **self._kwargs) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/modeller/common.py"", line 704, in threaded_run raise UserError(""Modeller execution failed; output and errors in log"") chimerax.core.errors.UserError: Modeller execution failed; output and errors in log > ui tool show ""Modeller Comparative"" > modeller comparative ""bp7 [1]:1"" numModels 2 fast false multichain true > hetPreserve false hydrogens false waterPreserve false executableLocation > /Library/modeller-10.4/modlib/modeller/__init__.py directory > /Users/jasonheld/Desktop 2023-07-30 13:22:15,979 WARNING Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/files 2023-07-30 13:23:59,151 WARNING Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/files Exception in thread Thread-1800: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973, in _bootstrap_inner self.run() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910, in run self._target(*self._args, **self._kwargs) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/modeller/common.py"", line 692, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py"", line 505, in run with Popen(*popenargs, **kwargs) as process: File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py"", line 951, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py"", line 1821, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) PermissionError: [Errno 13] Permission denied: '/Library/modeller-10.4/modlib/modeller/__init__.py' > ui tool show ""Modeller Comparative"" > modeller comparative ""bp7 [1]:1"" numModels 2 fast false multichain true > hetPreserve false hydrogens false waterPreserve false executableLocation > /Library/modeller-10.4/bin/mod10.4 directory /Users/jasonheld/Desktop > show #!1 models > hide #!1 models > modeller scores Missing or invalid ""structures"" argument: empty atom specifier > modeller scores 1 Missing or invalid ""structures"" argument: invalid atomic structures specifier > modeller scores #1 2023-07-30 13:38:51,299 WARNING Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /cxservices/api/v1/chimerax/jobs/V2AT7AYF0IV6EV9J/status 2023-07-30 13:38:51,306 WARNING Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/status > show #!1 models > ui tool show ""Modeller Comparative"" > modeller comparative ""bp7 [1]:1"" numModels 2 fast true multichain true > hetPreserve false hydrogens false waterPreserve false executableLocation > /Library/modeller-10.4/bin/mod10.4 directory /Users/jasonheld/Desktop 2023-07-30 14:10:44,471 WARNING Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /cxservices/api/v1/chimerax/jobs/V2AT7AYF0IV6EV9J/status 2023-07-30 14:12:00,141 WARNING Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /cxservices/api/v1/chimerax/jobs/V2AT7AYF0IV6EV9J/status > ui tool show ""Blast Protein"" 2023-07-30 14:16:42,612 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 60] Operation timed out')': /cxservices/api/v1/chimerax/jobs/V2AT7AYF0IV6EV9J/status 2023-07-30 14:16:42,778 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 60] Operation timed out')': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/status > ui tool show ""Blast Protein"" Alignment identifier is bp7 [2] Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment bp7 [2] Alignment identifier is bp7 [3] Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 4npq chain A to 4NPQ_A with 0 mismatches Associated 4npq chain B to 4NPQ_A with 0 mismatches Associated 4npq chain C to 4NPQ_A with 0 mismatches Associated 4npq chain D to 4NPQ_A with 0 mismatches Associated 4npq chain E to 4NPQ_A with 0 mismatches Associated 4npq chain F to 4NPQ_A with 0 mismatches Associated 4npq chain G to 4NPQ_A with 0 mismatches Associated 4npq chain H to 4NPQ_A with 0 mismatches Associated 4npq chain I to 4NPQ_A with 0 mismatches Associated 4npq chain J to 4NPQ_A with 0 mismatches Associated 4npq chain K to 4NPQ_A with 0 mismatches Associated 4npq chain L to 4NPQ_A with 0 mismatches Associated 4npq chain M to 4NPQ_A with 0 mismatches Associated 4npq chain N to 4NPQ_A with 0 mismatches Associated 4npq chain O to 4NPQ_A with 0 mismatches Associated 4npq chain P to 4NPQ_A with 0 mismatches Associated 4npq chain Q to 4NPQ_A with 0 mismatches Associated 4npq chain R to 4NPQ_A with 0 mismatches Associated 4npq chain S to 4NPQ_A with 0 mismatches Associated 4npq chain T to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Associated 6zgd chain A to 4NPQ_A with 0 mismatches Associated 6zgd chain B to 4NPQ_A with 0 mismatches Associated 6zgd chain C to 4NPQ_A with 0 mismatches Associated 6zgd chain D to 4NPQ_A with 0 mismatches Associated 6zgd chain E to 4NPQ_A with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment bp7 [3] 2023-07-30 14:32:52,914 WARNING Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError(""HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Read timed out. (read timeout=None)"")': /cxservices/api/v1/chimerax/jobs/V2AT7AYF0IV6EV9J/status 2023-07-30 14:32:52,915 WARNING Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError(""HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Read timed out. (read timeout=None)"")': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/status > ui tool show ""Modeller Comparative"" > modeller comparative ""bp7 [3]:1"" numModels 2 fast true multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/jasonheld/Desktop Webservices job id: OHN550A7YYFEN7XX 2023-07-30 14:56:13,169 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 60] Operation timed out')': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/status Modeller job (ID V2AT7AYF0IV6EV9J) finished Modeller failure with no error output OpenGL version: 4.1 ATI-4.12.7 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0) OS Loader Version: 577~170 Software: System Software Overview: System Version: macOS 13.4.1 (c) (22F770820d) Kernel Version: Darwin 22.5.0 Time since boot: 5 days, 18 hours, 11 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-020 Option ROM Version: 113-D32207P1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal VX2453 Series: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: SDA122202547 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.26 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.1.13 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Web Services fixed Eric Pettersen all ChimeraX