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Opened 2 years ago
Closed 2 years ago
#9483 closed defect (fixed)
No error message when timeout exceeded
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Web Services | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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('<urllib3.connection.HTTPConnection object at 0x7fd2bcd0d190>: 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 <listcomp>
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 <listcomp>
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' -> <chimerax.core.tasks.Tasks object at
0x7fd794b2d9d0>: 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 <listcomp>
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 <listcomp>
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>
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' -> <chimerax.core.tasks.Tasks object at
0x7fd794b2d9d0>: 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 <Signals.SIGABRT:
6>.
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('<urllib3.connection.HTTPConnection object at
0x7fd78d782a60>: 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('<urllib3.connection.HTTPConnection object at
0x7fd23ead6850>: 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('<urllib3.connection.HTTPConnection object at
0x7fd2bcd0d190>: 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
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pkginfo: 1.9.6
platformdirs: 3.5.0
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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
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requests: 2.28.2
scipy: 1.9.3
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Change History (5)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Web Services |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → No error message when timeout exceeded |
comment:2 by , 2 years ago
I don't think we should make the jobs longer. Our webservices don't scale dynamically with usage, and one instance runs at a time. There are 10 workers, so we can service at most 10 users at a time and if the workers are all busy it brings webservices to a halt for everyone. We're running them more or less as a courtesy, not for big data. We could discuss setting it up so we run webservices on every node with a load balancer in front.
I don't think any endpoint currently exists to get the runtime of a job -- so 'failed' or 'succeeded' is all we can know currently -- but we could add an endpoint to get the runtime. If it's at 3 hours and the job failed, going overtime is probably why.
comment:3 by , 2 years ago
As per the discussion in Scooter's office, "we" (read: Zach) are increasing the timeout to 6 hours, and the number of worker threads to 20 (if it's not already at least 20). Also investigate dynamic scaling.
Still need some kind of solution for communicating to the user that a failure was due to a timeout, but that is further down the road.
comment:4 by , 2 years ago
Increased timeout to six hours. Root owns the rq_workers script; Scooter or Greg will have to update it to spawn 20 workers.
comment:5 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
It looks like the script got changed to 20 workers at some point. Closing this ticket and opening another one for the remaining improvements so that the original reporter is not bothered by further updates.
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Hi Zach,
--Eric