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Opened 2 years ago
Closed 2 years ago
#9484 closed defect (fixed)
Unable to save session because ModellerWebJob class not found
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| 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 modeller comp using locally installed modeller. Error log below. I assumed local would work since the Modeller webserver is not working. I can run modeller with python on my local machine, so the issue is with ChimeraX.
modeller comparative "bp7 [3]:1" numModels 2 fast true multichain true hetPreserve false hydrogens false waterPreserve false executableLocation /Library/modeller-10.4/bin/mod10.4 directory /Users/jasonheld/Desktop2023-07-30 15:33:45,844 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', ConnectionResetError(54, 'Connection reset by peer'))': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/status
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
> ui tool show "Modeller Comparative"
> modeller comparative "bp7 [3]: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 15:33:45,844 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'ProtocolError('Connection aborted.', ConnectionResetError(54, 'Connection
reset by peer'))': /cxservices/api/v1/chimerax/jobs/AN4ZDIPBXTZ47A8R/status
> help help:contact.html
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, 17 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
VX2453 Series:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: SDA122202547
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.26
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.1.13
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (3)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unable to save session because ModellerWebJob class not found |
comment:3 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Saving a session now works with a running Modeller job without throwing an error. The job will not be restored when the session is restored -- that's ticket #7094.
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Hi Jason,
--Eric