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Opened 2 years ago
Closed 19 months ago
#9523 closed defect (fixed)
ISOLDE ResidueStepper holding reference to dead structure
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | 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
Just trying to save my ChimeraX session, nothing special.
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold.cxs
Log from Fri Aug 4 11:27:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold.cxs
Log from Fri Aug 4 11:20:04 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates.cxs
Log from Tue Aug 1 13:06:02 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates.cxs
Log from Tue Aug 1 13:01:50 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates.cxs
Log from Tue Aug 1 11:00:15 2023UCSF 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
> TQLLSSVLDRLTNRTTYDKRLRPRYGEKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFI
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 400 version None name bp1
Webservices job id: WIK3D25KZ97OHA44
> 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:6BE1
6be1 title:
Cryo-EM structure of serotonin receptor [more info...]
Chain information for 6be1 #2
---
Chain | Description | UniProt
A B C D E | 5-hydroxytryptamine receptor 3A | E9QLC0_MOUSE 6-462
Non-standard residues in 6be1 #2
---
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
6his title:
Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation [more
info...]
Chain information for 6his #3
---
Chain | Description | UniProt
A B C D E | 5-hydroxytryptamine receptor 3A | 5HT3A_MOUSE 8-458
Non-standard residues in 6his #3
---
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 #4
---
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 #4
---
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 #5
---
Chain | Description | UniProt
A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-325 329-362
Non-standard residues in 6pxd #5
---
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 #6
---
Chain | Description | UniProt
A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE 1-444
Non-standard residues in 6ubs #6
---
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
6uwz title:
Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-
bungarotoxin [more info...]
Chain information for 6uwz #7
---
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 #7
---
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:7SMM
7smm title:
Cryo-EM structure of Torpedo acetylcholine receptor in apo form [more info...]
Chain information for 7smm #8
---
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 #8
---
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 bp1 [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 6be1 chain A to 6HIS_A with 0 mismatches
Associated 6be1 chain B to 6HIS_A with 0 mismatches
Associated 6be1 chain C to 6HIS_A with 0 mismatches
Associated 6be1 chain D to 6HIS_A with 0 mismatches
Associated 6be1 chain E to 6HIS_A with 0 mismatches
Associated 6his chain A to 6HIS_A with 0 mismatches
Associated 6his chain E to 6HIS_A with 0 mismatches
Associated 6his chain B to 6HIS_A with 0 mismatches
Associated 6his chain C to 6HIS_A with 0 mismatches
Associated 6his chain D to 6HIS_A with 0 mismatches
Associated 6hug chain A to 6HUG_A with 0 mismatches
Associated 6hug chain D to 6HUG_A with 0 mismatches
Associated 6pxd chain E to 6PXD_A with 0 mismatches
Associated 6pxd chain A to 6PXD_A with 0 mismatches
Associated 6pxd chain B to 6PXD_A with 0 mismatches
Associated 6pxd chain C to 6PXD_A with 0 mismatches
Associated 6pxd chain D to 6PXD_A with 0 mismatches
Associated 6ubs chain A to 6UBS_A with 0 mismatches
Associated 6ubs chain B to 6UBS_A with 0 mismatches
Associated 6ubs chain C to 6UBS_A with 0 mismatches
Associated 6ubs chain D to 6UBS_A with 0 mismatches
Associated 6ubs chain E to 6UBS_A with 0 mismatches
Associated 6uwz chain A to 7SMM_A with 0 mismatches
Associated 6uwz chain D to 7SMM_A with 0 mismatches
Associated 7smm chain A to 7SMM_A with 0 mismatches
Associated 7smm chain D to 7SMM_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]
> sequence align "bp1 [1]" program clustalOmega replace true
Webservices job id: L6U5H4ZY04AMAQOA
> modeller comparative "bp1 [1]:1" numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false block true
> executableLocation /Library/modeller-10.4/bin/mod10.4 directory
> /Users/jasonheld/Desktop
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 541
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 533.2
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 554.7
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 537.1
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 522.3
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 534.8
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 519
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 549.1
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 520.3
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 541.6
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 534.1
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 511.9
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 528.5
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 509.3
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 540.1
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 567.7
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 522.2
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 536.7
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 532.9
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 517.7
RMSD between 4977 pruned atom pairs is 1.009 angstroms; (across all 5974
pairs: 3.672)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 543.7
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 559.1
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 533.3
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 535.5
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 551.5
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 548.4
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 506.3
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 518.5
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 528.3
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 538.5
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 544.1
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 525.7
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 522.7
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 544.9
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 527.7
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 561.9
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 534.4
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 543.5
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 540.5
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 522.2
RMSD between 4757 pruned atom pairs is 1.069 angstroms; (across all 5982
pairs: 3.472)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 523.6
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 530.2
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 540.3
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 547.8
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 541.6
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 556.6
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 530
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 527.7
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 534.1
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 534.3
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 521.1
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 528.7
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 533.4
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 549.9
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 526.5
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 558.9
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 534.3
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 552.7
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 545.1
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 511.5
RMSD between 4801 pruned atom pairs is 1.051 angstroms; (across all 5994
pairs: 3.179)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 538.8
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 541.6
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 516.9
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 520.3
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 543.7
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 557.8
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 545.7
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 547.3
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 540.4
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 541.9
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 548.7
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 510.7
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 529.9
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 515.3
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 538.5
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 559.9
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 520.5
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 546.9
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 542.7
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 521.9
RMSD between 5259 pruned atom pairs is 0.893 angstroms; (across all 5999
pairs: 2.936)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 535.2
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 526.9
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 549.3
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 540.9
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 515.7
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 573.2
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 543.5
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 502.7
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 543.2
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 548.5
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 549.6
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 529.9
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 536.6
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 534.5
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 525.9
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 546.2
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 529.9
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 552.1
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 534.9
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 514.1
RMSD between 4712 pruned atom pairs is 1.083 angstroms; (across all 5991
pairs: 3.298)
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Chain information for query
---
Chain | Description
9.1/A 9.2/A 9.3/A 9.4/A 9.5/A 9.1/B 9.2/B 9.3/B 9.4/B 9.5/B 9.1/C 9.2/C 9.3/C
9.4/C 9.5/C 9.1/D 9.2/D 9.3/D 9.4/D 9.5/D 9.1/E 9.2/E 9.3/E 9.4/E 9.5/E 9.1/F
9.2/F 9.3/F 9.4/F 9.5/F 9.1/G 9.2/G 9.3/G 9.4/G 9.5/G 9.1/H 9.2/H 9.3/H 9.4/H
9.5/H 9.1/I 9.2/I 9.3/I 9.4/I 9.5/I 9.1/J 9.2/J 9.3/J 9.4/J 9.5/J 9.1/K 9.2/K
9.3/K 9.4/K 9.5/K 9.1/L 9.2/L 9.3/L 9.4/L 9.5/L 9.1/M 9.2/M 9.3/M 9.4/M 9.5/M
9.1/N 9.2/N 9.3/N 9.4/N 9.5/N 9.1/O 9.2/O 9.3/O 9.4/O 9.5/O 9.1/P 9.2/P 9.3/P
9.4/P 9.5/P 9.1/Q 9.2/Q 9.3/Q 9.4/Q 9.5/Q 9.1/R 9.2/R 9.3/R 9.4/R 9.5/R 9.1/S
9.2/S 9.3/S 9.4/S 9.5/S 9.1/T 9.2/T 9.3/T 9.4/T 9.5/T | No description
available
> save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates.cxs
——— End of log from Tue Aug 1 11:00:15 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:8
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:5-8
27 atoms, 28 bonds, 4 residues, 1 model selected
> 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 #9.1 models
> hide #9.2 models
> hide #9.3 models
> hide #9.4 models
> hide #9.5 models
> show #!1 models
> select add #1
45859 atoms, 47110 bonds, 7 pseudobonds, 6198 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #1/A:7
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:5-7
20 atoms, 20 bonds, 3 residues, 1 model selected
> show sel atoms
> sequence align "bp1 [1]" program muscle
Alignment identifier is 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 6be1 chain A to 6HIS_A with 0 mismatches
Associated 6be1 chain B to 6HIS_A with 0 mismatches
Associated 6be1 chain C to 6HIS_A with 0 mismatches
Associated 6be1 chain D to 6HIS_A with 0 mismatches
Associated 6be1 chain E to 6HIS_A with 0 mismatches
Associated 6his chain A to 6HIS_A with 0 mismatches
Associated 6his chain E to 6HIS_A with 0 mismatches
Associated 6his chain B to 6HIS_A with 0 mismatches
Associated 6his chain C to 6HIS_A with 0 mismatches
Associated 6his chain D to 6HIS_A with 0 mismatches
Associated 6hug chain A to 6HUG_A with 0 mismatches
Associated 6hug chain D to 6HUG_A with 0 mismatches
Associated 6pxd chain E to 6PXD_A with 0 mismatches
Associated 6pxd chain A to 6PXD_A with 0 mismatches
Associated 6pxd chain B to 6PXD_A with 0 mismatches
Associated 6pxd chain C to 6PXD_A with 0 mismatches
Associated 6pxd chain D to 6PXD_A with 0 mismatches
Associated 6ubs chain A to 6UBS_A with 0 mismatches
Associated 6ubs chain B to 6UBS_A with 0 mismatches
Associated 6ubs chain C to 6UBS_A with 0 mismatches
Associated 6ubs chain D to 6UBS_A with 0 mismatches
Associated 6ubs chain E to 6UBS_A with 0 mismatches
Associated 6uwz chain A to 7SMM_A with 0 mismatches
Associated 6uwz chain D to 7SMM_A with 0 mismatches
Associated 7smm chain A to 7SMM_A with 0 mismatches
Associated 7smm chain D to 7SMM_A with 0 mismatches
Associated query (9.1) chain A to query with 0 mismatches
Associated query (9.1) chain B to query with 0 mismatches
Associated query (9.1) chain C to query with 0 mismatches
Associated query (9.1) chain D to query with 0 mismatches
Associated query (9.1) chain E to query with 0 mismatches
Associated query (9.1) chain F to query with 0 mismatches
Associated query (9.1) chain G to query with 0 mismatches
Associated query (9.1) chain H to query with 0 mismatches
Associated query (9.1) chain I to query with 0 mismatches
Associated query (9.1) chain J to query with 0 mismatches
Associated query (9.1) chain K to query with 0 mismatches
Associated query (9.1) chain L to query with 0 mismatches
Associated query (9.1) chain M to query with 0 mismatches
Associated query (9.1) chain N to query with 0 mismatches
Associated query (9.1) chain O to query with 0 mismatches
Associated query (9.1) chain P to query with 0 mismatches
Associated query (9.1) chain Q to query with 0 mismatches
Associated query (9.1) chain R to query with 0 mismatches
Associated query (9.1) chain S to query with 0 mismatches
Associated query (9.1) chain T to query with 0 mismatches
Associated query (9.2) chain A to query with 0 mismatches
Associated query (9.2) chain B to query with 0 mismatches
Associated query (9.2) chain C to query with 0 mismatches
Associated query (9.2) chain D to query with 0 mismatches
Associated query (9.2) chain E to query with 0 mismatches
Associated query (9.2) chain F to query with 0 mismatches
Associated query (9.2) chain G to query with 0 mismatches
Associated query (9.2) chain H to query with 0 mismatches
Associated query (9.2) chain I to query with 0 mismatches
Associated query (9.2) chain J to query with 0 mismatches
Associated query (9.2) chain K to query with 0 mismatches
Associated query (9.2) chain L to query with 0 mismatches
Associated query (9.2) chain M to query with 0 mismatches
Associated query (9.2) chain N to query with 0 mismatches
Associated query (9.2) chain O to query with 0 mismatches
Associated query (9.2) chain P to query with 0 mismatches
Associated query (9.2) chain Q to query with 0 mismatches
Associated query (9.2) chain R to query with 0 mismatches
Associated query (9.2) chain S to query with 0 mismatches
Associated query (9.2) chain T to query with 0 mismatches
Associated query (9.3) chain A to query with 0 mismatches
Associated query (9.3) chain B to query with 0 mismatches
Associated query (9.3) chain C to query with 0 mismatches
Associated query (9.3) chain D to query with 0 mismatches
Associated query (9.3) chain E to query with 0 mismatches
Associated query (9.3) chain F to query with 0 mismatches
Associated query (9.3) chain G to query with 0 mismatches
Associated query (9.3) chain H to query with 0 mismatches
Associated query (9.3) chain I to query with 0 mismatches
Associated query (9.3) chain J to query with 0 mismatches
Associated query (9.3) chain K to query with 0 mismatches
Associated query (9.3) chain L to query with 0 mismatches
Associated query (9.3) chain M to query with 0 mismatches
Associated query (9.3) chain N to query with 0 mismatches
Associated query (9.3) chain O to query with 0 mismatches
Associated query (9.3) chain P to query with 0 mismatches
Associated query (9.3) chain Q to query with 0 mismatches
Associated query (9.3) chain R to query with 0 mismatches
Associated query (9.3) chain S to query with 0 mismatches
Associated query (9.3) chain T to query with 0 mismatches
Associated query (9.4) chain A to query with 0 mismatches
Associated query (9.4) chain B to query with 0 mismatches
Associated query (9.4) chain C to query with 0 mismatches
Associated query (9.4) chain D to query with 0 mismatches
Associated query (9.4) chain E to query with 0 mismatches
Associated query (9.4) chain F to query with 0 mismatches
Associated query (9.4) chain G to query with 0 mismatches
Associated query (9.4) chain H to query with 0 mismatches
Associated query (9.4) chain I to query with 0 mismatches
Associated query (9.4) chain J to query with 0 mismatches
Associated query (9.4) chain K to query with 0 mismatches
Associated query (9.4) chain L to query with 0 mismatches
Associated query (9.4) chain M to query with 0 mismatches
Associated query (9.4) chain N to query with 0 mismatches
Associated query (9.4) chain O to query with 0 mismatches
Associated query (9.4) chain P to query with 0 mismatches
Associated query (9.4) chain Q to query with 0 mismatches
Associated query (9.4) chain R to query with 0 mismatches
Associated query (9.4) chain S to query with 0 mismatches
Associated query (9.4) chain T to query with 0 mismatches
Associated query (9.5) chain A to query with 0 mismatches
Associated query (9.5) chain B to query with 0 mismatches
Associated query (9.5) chain C to query with 0 mismatches
Associated query (9.5) chain D to query with 0 mismatches
Associated query (9.5) chain E to query with 0 mismatches
Associated query (9.5) chain F to query with 0 mismatches
Associated query (9.5) chain G to query with 0 mismatches
Associated query (9.5) chain H to query with 0 mismatches
Associated query (9.5) chain I to query with 0 mismatches
Associated query (9.5) chain J to query with 0 mismatches
Associated query (9.5) chain K to query with 0 mismatches
Associated query (9.5) chain L to query with 0 mismatches
Associated query (9.5) chain M to query with 0 mismatches
Associated query (9.5) chain N to query with 0 mismatches
Associated query (9.5) chain O to query with 0 mismatches
Associated query (9.5) chain P to query with 0 mismatches
Associated query (9.5) chain Q to query with 0 mismatches
Associated query (9.5) chain R to query with 0 mismatches
Associated query (9.5) chain S to query with 0 mismatches
Associated query (9.5) chain T to query with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Webservices job id: S63YDQE2T5NUVODF
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select
> #5/A:53-64,73-85,99-101,114-116,119-123,132-136,141-153,165-174,182-186,192-194,203-205,210-213,216-217,222-223,225-234
798 atoms, 801 bonds, 93 residues, 1 model selected
> show #!1 atoms
> hide #!1 atoms
> select #5/A:25
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:25-29
38 atoms, 39 bonds, 5 residues, 1 model selected
> show #!1 atoms
> hide #!1 atoms
> select #5/A:40-41
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/A:25-41
129 atoms, 131 bonds, 17 residues, 1 model selected
> show #!1 atoms
> hide #!1 atoms
> select #5/A:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:44-51
65 atoms, 67 bonds, 8 residues, 1 model selected
> show #!1 atoms
> hide #!1 atoms
> select #5/A:55-56
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/A:55-131
631 atoms, 648 bonds, 77 residues, 1 model selected
> show #!1 atoms
[Repeated 1 time(s)]
> hide #!1 atoms
> select add #5
13844 atoms, 14205 bonds, 1714 residues, 1 model selected
> select subtract #5
Nothing selected
> hide #!1 models
> select #5/A:25-77
412 atoms, 421 bonds, 53 residues, 1 model selected
> select #5/A:25-264
1957 atoms, 2009 bonds, 240 residues, 1 model selected
> show #5 models
> hide sel atoms
> select add #5
13844 atoms, 14205 bonds, 1714 residues, 1 model selected
> hide sel atoms
> select #5/A:25-196
1381 atoms, 1415 bonds, 172 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #5/A:25-26
12 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> close session
> ui tool show "Blast Protein"
> blastprotein
> KPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGSLDLGLSKEIDSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIEGDGTVYTSQRLTVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKKSVSTESYELPQFVLQSIKVVNHTQKLSSGEYSRLCWFFLFKRNIGFYIIQIYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSSMPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKSQPARAANIDKYSRSLFPSIFVLFNVGYWAYFI
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 400 version None name bp4
Webservices job id: 0HZUUJA9I07VBX4C
> 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:6BE1
6be1 title:
Cryo-EM structure of serotonin receptor [more info...]
Chain information for 6be1 #2
---
Chain | Description | UniProt
A B C D E | 5-hydroxytryptamine receptor 3A | E9QLC0_MOUSE 6-462
Non-standard residues in 6be1 #2
---
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
6his title:
Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation [more
info...]
Chain information for 6his #3
---
Chain | Description | UniProt
A B C D E | 5-hydroxytryptamine receptor 3A | 5HT3A_MOUSE 8-458
Non-standard residues in 6his #3
---
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 #4
---
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 #4
---
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 #5
---
Chain | Description | UniProt
A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-325 329-362
Non-standard residues in 6pxd #5
---
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 #6
---
Chain | Description | UniProt
A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE 1-444
Non-standard residues in 6ubs #6
---
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
6uwz title:
Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-
bungarotoxin [more info...]
Chain information for 6uwz #7
---
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 #7
---
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 #8
---
Chain | Description | UniProt
A B C D E | Proton-gated ion channel | GLIC_GLOVI 2-317
> select clear
> open pdb:7SMM
7smm title:
Cryo-EM structure of Torpedo acetylcholine receptor in apo form [more info...]
Chain information for 7smm #9
---
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 #9
---
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 bp4 [1]
Associated 4npq chain A to 6ZGD_A with 0 mismatches
Associated 4npq chain B to 6ZGD_A with 0 mismatches
Associated 4npq chain C to 6ZGD_A with 0 mismatches
Associated 4npq chain D to 6ZGD_A with 0 mismatches
Associated 4npq chain E to 6ZGD_A with 0 mismatches
Associated 4npq chain F to 6ZGD_A with 0 mismatches
Associated 4npq chain G to 6ZGD_A with 0 mismatches
Associated 4npq chain H to 6ZGD_A with 0 mismatches
Associated 4npq chain I to 6ZGD_A with 0 mismatches
Associated 4npq chain J to 6ZGD_A with 0 mismatches
Associated 4npq chain K to 6ZGD_A with 0 mismatches
Associated 4npq chain L to 6ZGD_A with 0 mismatches
Associated 4npq chain M to 6ZGD_A with 0 mismatches
Associated 4npq chain N to 6ZGD_A with 0 mismatches
Associated 4npq chain O to 6ZGD_A with 0 mismatches
Associated 4npq chain P to 6ZGD_A with 0 mismatches
Associated 4npq chain Q to 6ZGD_A with 0 mismatches
Associated 4npq chain R to 6ZGD_A with 0 mismatches
Associated 4npq chain S to 6ZGD_A with 0 mismatches
Associated 4npq chain T to 6ZGD_A with 0 mismatches
Associated 6be1 chain A to 6HIS_A with 0 mismatches
Associated 6be1 chain B to 6HIS_A with 0 mismatches
Associated 6be1 chain C to 6HIS_A with 0 mismatches
Associated 6be1 chain D to 6HIS_A with 0 mismatches
Associated 6be1 chain E to 6HIS_A with 0 mismatches
Associated 6his chain A to 6HIS_A with 0 mismatches
Associated 6his chain E to 6HIS_A with 0 mismatches
Associated 6his chain B to 6HIS_A with 0 mismatches
Associated 6his chain C to 6HIS_A with 0 mismatches
Associated 6his chain D to 6HIS_A with 0 mismatches
Associated 6hug chain A to 6HUG_A with 0 mismatches
Associated 6hug chain D to 6HUG_A with 0 mismatches
Associated 6pxd chain E to 6PXD_A with 0 mismatches
Associated 6pxd chain A to 6PXD_A with 0 mismatches
Associated 6pxd chain B to 6PXD_A with 0 mismatches
Associated 6pxd chain C to 6PXD_A with 0 mismatches
Associated 6pxd chain D to 6PXD_A with 0 mismatches
Associated 6ubs chain A to 6UBS_A with 0 mismatches
Associated 6ubs chain B to 6UBS_A with 0 mismatches
Associated 6ubs chain C to 6UBS_A with 0 mismatches
Associated 6ubs chain D to 6UBS_A with 0 mismatches
Associated 6ubs chain E to 6UBS_A with 0 mismatches
Associated 6uwz chain A to 7SMM_A with 0 mismatches
Associated 6uwz chain D to 7SMM_A with 0 mismatches
Associated 6zgd chain A to 6ZGD_A with 0 mismatches
Associated 6zgd chain B to 6ZGD_A with 0 mismatches
Associated 6zgd chain C to 6ZGD_A with 0 mismatches
Associated 6zgd chain D to 6ZGD_A with 0 mismatches
Associated 6zgd chain E to 6ZGD_A with 0 mismatches
Associated 7smm chain A to 7SMM_A with 0 mismatches
Associated 7smm chain D to 7SMM_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp4 [1]
Alignment identifier is bp4 [2]
Associated 4npq chain A to 6ZGD_A with 0 mismatches
Associated 4npq chain B to 6ZGD_A with 0 mismatches
Associated 4npq chain C to 6ZGD_A with 0 mismatches
Associated 4npq chain D to 6ZGD_A with 0 mismatches
Associated 4npq chain E to 6ZGD_A with 0 mismatches
Associated 4npq chain F to 6ZGD_A with 0 mismatches
Associated 4npq chain G to 6ZGD_A with 0 mismatches
Associated 4npq chain H to 6ZGD_A with 0 mismatches
Associated 4npq chain I to 6ZGD_A with 0 mismatches
Associated 4npq chain J to 6ZGD_A with 0 mismatches
Associated 4npq chain K to 6ZGD_A with 0 mismatches
Associated 4npq chain L to 6ZGD_A with 0 mismatches
Associated 4npq chain M to 6ZGD_A with 0 mismatches
Associated 4npq chain N to 6ZGD_A with 0 mismatches
Associated 4npq chain O to 6ZGD_A with 0 mismatches
Associated 4npq chain P to 6ZGD_A with 0 mismatches
Associated 4npq chain Q to 6ZGD_A with 0 mismatches
Associated 4npq chain R to 6ZGD_A with 0 mismatches
Associated 4npq chain S to 6ZGD_A with 0 mismatches
Associated 4npq chain T to 6ZGD_A with 0 mismatches
Associated 6be1 chain A to 6HIS_A with 0 mismatches
Associated 6be1 chain B to 6HIS_A with 0 mismatches
Associated 6be1 chain C to 6HIS_A with 0 mismatches
Associated 6be1 chain D to 6HIS_A with 0 mismatches
Associated 6be1 chain E to 6HIS_A with 0 mismatches
Associated 6his chain A to 6HIS_A with 0 mismatches
Associated 6his chain E to 6HIS_A with 0 mismatches
Associated 6his chain B to 6HIS_A with 0 mismatches
Associated 6his chain C to 6HIS_A with 0 mismatches
Associated 6his chain D to 6HIS_A with 0 mismatches
Associated 6hug chain A to 6HUG_A with 0 mismatches
Associated 6hug chain D to 6HUG_A with 0 mismatches
Associated 6pxd chain E to 6PXD_A with 0 mismatches
Associated 6pxd chain A to 6PXD_A with 0 mismatches
Associated 6pxd chain B to 6PXD_A with 0 mismatches
Associated 6pxd chain C to 6PXD_A with 0 mismatches
Associated 6pxd chain D to 6PXD_A with 0 mismatches
Associated 6ubs chain A to 6UBS_A with 0 mismatches
Associated 6ubs chain B to 6UBS_A with 0 mismatches
Associated 6ubs chain C to 6UBS_A with 0 mismatches
Associated 6ubs chain D to 6UBS_A with 0 mismatches
Associated 6ubs chain E to 6UBS_A with 0 mismatches
Associated 6uwz chain A to 7SMM_A with 0 mismatches
Associated 6uwz chain D to 7SMM_A with 0 mismatches
Associated 6zgd chain A to 6ZGD_A with 0 mismatches
Associated 6zgd chain B to 6ZGD_A with 0 mismatches
Associated 6zgd chain C to 6ZGD_A with 0 mismatches
Associated 6zgd chain D to 6ZGD_A with 0 mismatches
Associated 6zgd chain E to 6ZGD_A with 0 mismatches
Associated 7smm chain A to 7SMM_A with 0 mismatches
Associated 7smm chain D to 7SMM_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp4 [2]
Alignment identifier is bp4 [3]
Associated 4npq chain A to 6ZGD_A with 0 mismatches
Associated 4npq chain B to 6ZGD_A with 0 mismatches
Associated 4npq chain C to 6ZGD_A with 0 mismatches
Associated 4npq chain D to 6ZGD_A with 0 mismatches
Associated 4npq chain E to 6ZGD_A with 0 mismatches
Associated 4npq chain F to 6ZGD_A with 0 mismatches
Associated 4npq chain G to 6ZGD_A with 0 mismatches
Associated 4npq chain H to 6ZGD_A with 0 mismatches
Associated 4npq chain I to 6ZGD_A with 0 mismatches
Associated 4npq chain J to 6ZGD_A with 0 mismatches
Associated 4npq chain K to 6ZGD_A with 0 mismatches
Associated 4npq chain L to 6ZGD_A with 0 mismatches
Associated 4npq chain M to 6ZGD_A with 0 mismatches
Associated 4npq chain N to 6ZGD_A with 0 mismatches
Associated 4npq chain O to 6ZGD_A with 0 mismatches
Associated 4npq chain P to 6ZGD_A with 0 mismatches
Associated 4npq chain Q to 6ZGD_A with 0 mismatches
Associated 4npq chain R to 6ZGD_A with 0 mismatches
Associated 4npq chain S to 6ZGD_A with 0 mismatches
Associated 4npq chain T to 6ZGD_A with 0 mismatches
Associated 6be1 chain A to 6HIS_A with 0 mismatches
Associated 6be1 chain B to 6HIS_A with 0 mismatches
Associated 6be1 chain C to 6HIS_A with 0 mismatches
Associated 6be1 chain D to 6HIS_A with 0 mismatches
Associated 6be1 chain E to 6HIS_A with 0 mismatches
Associated 6his chain A to 6HIS_A with 0 mismatches
Associated 6his chain E to 6HIS_A with 0 mismatches
Associated 6his chain B to 6HIS_A with 0 mismatches
Associated 6his chain C to 6HIS_A with 0 mismatches
Associated 6his chain D to 6HIS_A with 0 mismatches
Associated 6hug chain A to 6HUG_A with 0 mismatches
Associated 6hug chain D to 6HUG_A with 0 mismatches
Associated 6pxd chain E to 6PXD_A with 0 mismatches
Associated 6pxd chain A to 6PXD_A with 0 mismatches
Associated 6pxd chain B to 6PXD_A with 0 mismatches
Associated 6pxd chain C to 6PXD_A with 0 mismatches
Associated 6pxd chain D to 6PXD_A with 0 mismatches
Associated 6ubs chain A to 6UBS_A with 0 mismatches
Associated 6ubs chain B to 6UBS_A with 0 mismatches
Associated 6ubs chain C to 6UBS_A with 0 mismatches
Associated 6ubs chain D to 6UBS_A with 0 mismatches
Associated 6ubs chain E to 6UBS_A with 0 mismatches
Associated 6uwz chain A to 7SMM_A with 0 mismatches
Associated 6uwz chain D to 7SMM_A with 0 mismatches
Associated 6zgd chain A to 6ZGD_A with 0 mismatches
Associated 6zgd chain B to 6ZGD_A with 0 mismatches
Associated 6zgd chain C to 6ZGD_A with 0 mismatches
Associated 6zgd chain D to 6ZGD_A with 0 mismatches
Associated 6zgd chain E to 6ZGD_A with 0 mismatches
Associated 7smm chain A to 7SMM_A with 0 mismatches
Associated 7smm chain D to 7SMM_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp4 [3]
> sequence align "bp4 [3]" program clustalOmega replace true
Webservices job id: LSJ08VRIBKQX7FDR
> modeller comparative "bp4 [3]:1" numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false block true
> executableLocation /Library/modeller-10.4/bin/mod10.4 directory
> /Users/jasonheld/Desktop
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 521.3
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 546.8
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 537.2
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 541.4
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 534.3
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 554.7
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 521.1
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 517.4
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 546.8
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 533.1
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 519.8
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 533.9
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 518.2
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 540.4
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 520
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 553
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 523
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 531.5
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 553.4
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 507.6
RMSD between 3811 pruned atom pairs is 1.182 angstroms; (across all 5818
pairs: 3.160)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 514.9
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 532.1
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 539
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 520.8
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 540.4
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 540.6
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 522.7
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 523.6
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 539
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 523.8
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 524.8
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 540.2
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 535.4
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 529.6
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 535
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 557.2
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 522.8
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 533.8
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 526.7
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 517.4
RMSD between 3517 pruned atom pairs is 1.314 angstroms; (across all 5824
pairs: 3.191)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 519.9
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 533.2
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 519.6
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 538.6
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 549.1
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 543.4
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 511.3
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 549.2
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 546.9
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 530.2
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 529
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 513.2
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 541.3
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 537.4
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 528.7
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 536.9
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 535.1
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 545.6
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 522.3
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 524.6
RMSD between 4490 pruned atom pairs is 1.022 angstroms; (across all 5816
pairs: 2.866)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 517.9
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 519.5
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 536
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 548.6
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 534.5
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 557.7
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 511
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 519
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 522.4
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 544.6
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 543.2
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 538.9
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 516.6
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 525.8
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 534.8
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 546.4
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 542.8
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 545.6
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 527.8
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 507.6
RMSD between 4903 pruned atom pairs is 1.060 angstroms; (across all 5825
pairs: 2.952)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain A (#1) with query, chain A (#), sequence alignment
score = 525.6
Matchmaker 4npq, chain B (#1) with query, chain B (#), sequence alignment
score = 556.2
Matchmaker 4npq, chain C (#1) with query, chain C (#), sequence alignment
score = 533
Matchmaker 4npq, chain D (#1) with query, chain D (#), sequence alignment
score = 533.1
Matchmaker 4npq, chain E (#1) with query, chain E (#), sequence alignment
score = 541.9
Matchmaker 4npq, chain F (#1) with query, chain F (#), sequence alignment
score = 542.1
Matchmaker 4npq, chain G (#1) with query, chain G (#), sequence alignment
score = 522
Matchmaker 4npq, chain H (#1) with query, chain H (#), sequence alignment
score = 516.4
Matchmaker 4npq, chain I (#1) with query, chain I (#), sequence alignment
score = 524.6
Matchmaker 4npq, chain J (#1) with query, chain J (#), sequence alignment
score = 535
Matchmaker 4npq, chain K (#1) with query, chain K (#), sequence alignment
score = 529
Matchmaker 4npq, chain L (#1) with query, chain L (#), sequence alignment
score = 538.4
Matchmaker 4npq, chain M (#1) with query, chain M (#), sequence alignment
score = 519.2
Matchmaker 4npq, chain N (#1) with query, chain N (#), sequence alignment
score = 530.2
Matchmaker 4npq, chain O (#1) with query, chain O (#), sequence alignment
score = 527.8
Matchmaker 4npq, chain P (#1) with query, chain P (#), sequence alignment
score = 555
Matchmaker 4npq, chain Q (#1) with query, chain Q (#), sequence alignment
score = 520.4
Matchmaker 4npq, chain R (#1) with query, chain R (#), sequence alignment
score = 543.2
Matchmaker 4npq, chain S (#1) with query, chain S (#), sequence alignment
score = 538
Matchmaker 4npq, chain T (#1) with query, chain T (#), sequence alignment
score = 528.2
RMSD between 4517 pruned atom pairs is 1.188 angstroms; (across all 5823
pairs: 3.019)
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Associated query chain A to query with 0 mismatches
Associated query chain B to query with 0 mismatches
Associated query chain C to query with 0 mismatches
Associated query chain D to query with 0 mismatches
Associated query chain E to query with 0 mismatches
Associated query chain F to query with 0 mismatches
Associated query chain G to query with 0 mismatches
Associated query chain H to query with 0 mismatches
Associated query chain I to query with 0 mismatches
Associated query chain J to query with 0 mismatches
Associated query chain K to query with 0 mismatches
Associated query chain L to query with 0 mismatches
Associated query chain M to query with 0 mismatches
Associated query chain N to query with 0 mismatches
Associated query chain O to query with 0 mismatches
Associated query chain P to query with 0 mismatches
Associated query chain Q to query with 0 mismatches
Associated query chain R to query with 0 mismatches
Associated query chain S to query with 0 mismatches
Associated query chain T to query with 0 mismatches
Chain information for query
---
Chain | Description
10.1/A 10.2/A 10.3/A 10.4/A 10.5/A 10.1/B 10.2/B 10.3/B 10.4/B 10.5/B 10.1/C
10.2/C 10.3/C 10.4/C 10.5/C 10.1/D 10.2/D 10.3/D 10.4/D 10.5/D 10.1/E 10.2/E
10.3/E 10.4/E 10.5/E 10.1/F 10.2/F 10.3/F 10.4/F 10.5/F 10.1/G 10.2/G 10.3/G
10.4/G 10.5/G 10.1/H 10.2/H 10.3/H 10.4/H 10.5/H 10.1/I 10.2/I 10.3/I 10.4/I
10.5/I 10.1/J 10.2/J 10.3/J 10.4/J 10.5/J 10.1/K 10.2/K 10.3/K 10.4/K 10.5/K
10.1/L 10.2/L 10.3/L 10.4/L 10.5/L 10.1/M 10.2/M 10.3/M 10.4/M 10.5/M 10.1/N
10.2/N 10.3/N 10.4/N 10.5/N 10.1/O 10.2/O 10.3/O 10.4/O 10.5/O 10.1/P 10.2/P
10.3/P 10.4/P 10.5/P 10.1/Q 10.2/Q 10.3/Q 10.4/Q 10.5/Q 10.1/R 10.2/R 10.3/R
10.4/R 10.5/R 10.1/S 10.2/S 10.3/S 10.4/S 10.5/S 10.1/T 10.2/T 10.3/T 10.4/T
10.5/T | No description available
> save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates.cxs
——— End of log from Tue Aug 1 13:01:50 2023 ———
opened ChimeraX session
> ui tool show "Renumber Residues"
> renumber #10.1/A-T #10.2/A-T #10.3/A-T #10.4/A-T #10.5/A-T seqStart 1
29640 residues renumbered
> save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates.cxs
——— End of log from Tue Aug 1 13:06:02 2023 ———
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #5#10.1-5#!1-3,6-9 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6hug, chain E (#4) with 6pxd, chain E (#5), sequence alignment
score = 819.5
RMSD between 221 pruned atom pairs is 1.222 angstroms; (across all 297 pairs:
2.189)
Matchmaker 6hug, chain E (#4) with query, chain A (#10.1), sequence alignment
score = 843.8
RMSD between 199 pruned atom pairs is 1.180 angstroms; (across all 275 pairs:
2.490)
Matchmaker 6hug, chain E (#4) with query, chain A (#10.2), sequence alignment
score = 821.6
RMSD between 199 pruned atom pairs is 1.150 angstroms; (across all 275 pairs:
2.525)
Matchmaker 6hug, chain E (#4) with query, chain A (#10.3), sequence alignment
score = 818.1
RMSD between 202 pruned atom pairs is 1.084 angstroms; (across all 275 pairs:
2.144)
Matchmaker 6hug, chain E (#4) with query, chain A (#10.4), sequence alignment
score = 825.3
RMSD between 215 pruned atom pairs is 1.091 angstroms; (across all 275 pairs:
2.321)
Matchmaker 6hug, chain E (#4) with query, chain A (#10.5), sequence alignment
score = 816.3
RMSD between 198 pruned atom pairs is 1.195 angstroms; (across all 275 pairs:
2.270)
Matchmaker 6hug, chain B (#4) with 4npq, chain L (#1), sequence alignment
score = 440.5
RMSD between 131 pruned atom pairs is 1.341 angstroms; (across all 258 pairs:
6.642)
Matchmaker 6hug, chain E (#4) with 6be1, chain C (#2), sequence alignment
score = 447
RMSD between 121 pruned atom pairs is 1.324 angstroms; (across all 323 pairs:
4.281)
Matchmaker 6hug, chain B (#4) with 6his, chain A (#3), sequence alignment
score = 501.2
RMSD between 171 pruned atom pairs is 1.324 angstroms; (across all 319 pairs:
3.838)
Matchmaker 6hug, chain E (#4) with 6ubs, chain A (#6), sequence alignment
score = 871.3
RMSD between 260 pruned atom pairs is 1.229 angstroms; (across all 326 pairs:
2.290)
Matchmaker 6hug, chain A (#4) with 6uwz, chain E (#7), sequence alignment
score = 466.4
RMSD between 183 pruned atom pairs is 1.378 angstroms; (across all 335 pairs:
4.074)
Matchmaker 6hug, chain B (#4) with 6zgd, chain A (#8), sequence alignment
score = 404.8
RMSD between 143 pruned atom pairs is 1.349 angstroms; (across all 245 pairs:
3.826)
Matchmaker 6hug, chain B (#4) with 7smm, chain C (#9), sequence alignment
score = 491.3
RMSD between 183 pruned atom pairs is 1.304 angstroms; (across all 322 pairs:
7.676)
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #5 models
> hide #!6 models
> close #10
> hide #!7 models
> hide #!8 models
> hide #!9 models
> save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold.cxs
——— End of log from Fri Aug 4 11:20:04 2023 ———
opened ChimeraX session
> select #4/G:472@NE
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
62 atoms, 62 bonds, 8 residues, 1 model selected
> select up
848 atoms, 870 bonds, 108 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/G:13@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
93 atoms, 92 bonds, 13 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold.cxs
> show #!1 models
> hide #!4 models
> show #!4 models
> select #1/H:187@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
67 atoms, 67 bonds, 8 residues, 1 model selected
> select up
1085 atoms, 1118 bonds, 134 residues, 1 model selected
> select up
1162 atoms, 1195 bonds, 149 residues, 1 model selected
> select up
2199 atoms, 2255 bonds, 309 residues, 1 model selected
> select up
45859 atoms, 47110 bonds, 6198 residues, 1 model selected
Drag select of 7431 atoms, 1 pseudobonds
Drag select of 9261 atoms, 2 pseudobonds
> select up
9598 atoms, 9830 bonds, 2 pseudobonds, 1316 residues, 2 models selected
> select up
10658 atoms, 10939 bonds, 2 pseudobonds, 1465 residues, 2 models selected
> select up
11260 atoms, 11562 bonds, 2 pseudobonds, 1549 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 10181 atoms, 1 pseudobonds
> select up
10483 atoms, 10747 bonds, 1 pseudobond, 1430 residues, 2 models selected
> select up
10887 atoms, 11181 bonds, 1 pseudobond, 1486 residues, 2 models selected
> select up
11335 atoms, 11644 bonds, 1 pseudobond, 1553 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 11650 atoms, 1 pseudobonds
Drag select of 1862 atoms
Drag select of 11583 atoms, 1 pseudobonds
> hide #!1 models
> show #!1 models
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 99 atoms, 19 pseudobonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #5 models
> hide #!3 models
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #5 models
> hide #1.1 models
> select #7/G:64@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
227 atoms, 235 bonds, 30 residues, 1 model selected
> select up
546 atoms, 565 bonds, 73 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/F:14@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
25 atoms, 24 bonds, 4 residues, 1 model selected
> select up
546 atoms, 565 bonds, 73 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold.cxs
Drag select of 31604 atoms, 10 pseudobonds, 1297 bonds
> ui tool show Matchmaker
> matchmaker #5#!2-4,6-9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4npq, chain N (#1) with 6pxd, chain E (#5), sequence alignment
score = 518.7
RMSD between 159 pruned atom pairs is 1.202 angstroms; (across all 303 pairs:
3.919)
Matchmaker 4npq, chain L (#1) with 6be1, chain C (#2), sequence alignment
score = 334.4
RMSD between 89 pruned atom pairs is 1.283 angstroms; (across all 282 pairs:
9.041)
Matchmaker 4npq, chain L (#1) with 6his, chain A (#3), sequence alignment
score = 397.6
RMSD between 101 pruned atom pairs is 1.247 angstroms; (across all 289 pairs:
9.826)
Matchmaker 4npq, chain L (#1) with 6hug, chain B (#4), sequence alignment
score = 440.5
RMSD between 131 pruned atom pairs is 1.341 angstroms; (across all 258 pairs:
6.642)
Matchmaker 4npq, chain L (#1) with 6ubs, chain A (#6), sequence alignment
score = 439
RMSD between 126 pruned atom pairs is 1.185 angstroms; (across all 289 pairs:
4.421)
Matchmaker 4npq, chain K (#1) with 6uwz, chain B (#7), sequence alignment
score = 410.8
RMSD between 140 pruned atom pairs is 1.224 angstroms; (across all 300 pairs:
7.088)
Matchmaker 4npq, chain O (#1) with 6zgd, chain A (#8), sequence alignment
score = 1481.1
RMSD between 266 pruned atom pairs is 0.948 angstroms; (across all 288 pairs:
1.311)
Matchmaker 4npq, chain N (#1) with 7smm, chain B (#9), sequence alignment
score = 436.7
RMSD between 172 pruned atom pairs is 1.244 angstroms; (across all 299 pairs:
6.728)
Drag select of 31604 atoms, 10 pseudobonds, 1297 bonds
> save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold.cxs
——— End of log from Fri Aug 4 11:27:00 2023 ———
opened ChimeraX session
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/modeller_multitemplate_1.pdb
Chain information for modeller_multitemplate_1.pdb #10
---
Chain | Description
A B C D E | No description available
> hide #!9 models
> hide #!4 models
> hide #10 models
> show #10 models
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
Chain information for
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
#11
---
Chain | Description
A | No description available
> ui tool show "Change Chain IDs"
> select add #11
36623 atoms, 6384 bonds, 10 pseudobonds, 4173 residues, 5 models selected
> select add #9
36623 atoms, 23300 bonds, 10 pseudobonds, 4173 residues, 5 models selected
> select subtract #9
19367 atoms, 5632 bonds, 5 pseudobonds, 2041 residues, 3 models selected
> select add #4
19367 atoms, 19838 bonds, 5 pseudobonds, 2041 residues, 3 models selected
> select subtract #4
5019 atoms, 5087 bonds, 312 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel A
Chain IDs of 0 residues changed
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #5,11#!1-4,6-9 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker modeller_multitemplate_1.pdb, chain A (#10) with 6pxd, chain E
(#5), sequence alignment score = 869.7
RMSD between 248 pruned atom pairs is 1.068 angstroms; (across all 306 pairs:
1.825)
Matchmaker modeller_multitemplate_1.pdb, chain A (#10) with
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb,
chain A (#11), sequence alignment score = 1542.7
RMSD between 200 pruned atom pairs is 1.278 angstroms; (across all 312 pairs:
2.488)
Matchmaker modeller_multitemplate_1.pdb, chain D (#10) with 4npq, chain N
(#1), sequence alignment score = 547.4
RMSD between 265 pruned atom pairs is 0.549 angstroms; (across all 292 pairs:
2.246)
Matchmaker modeller_multitemplate_1.pdb, chain C (#10) with 6be1, chain D
(#2), sequence alignment score = 399.6
RMSD between 76 pruned atom pairs is 1.466 angstroms; (across all 285 pairs:
10.670)
Matchmaker modeller_multitemplate_1.pdb, chain A (#10) with 6his, chain A
(#3), sequence alignment score = 463
RMSD between 89 pruned atom pairs is 0.970 angstroms; (across all 285 pairs:
9.535)
Matchmaker modeller_multitemplate_1.pdb, chain A (#10) with 6hug, chain E
(#4), sequence alignment score = 843.8
RMSD between 199 pruned atom pairs is 1.180 angstroms; (across all 275 pairs:
2.490)
Matchmaker modeller_multitemplate_1.pdb, chain A (#10) with 6ubs, chain A
(#6), sequence alignment score = 804.5
RMSD between 247 pruned atom pairs is 1.198 angstroms; (across all 299 pairs:
3.266)
Matchmaker modeller_multitemplate_1.pdb, chain C (#10) with 6uwz, chain B
(#7), sequence alignment score = 428.3
RMSD between 169 pruned atom pairs is 1.230 angstroms; (across all 294 pairs:
6.501)
Matchmaker modeller_multitemplate_1.pdb, chain D (#10) with 6zgd, chain A
(#8), sequence alignment score = 469.5
RMSD between 230 pruned atom pairs is 0.870 angstroms; (across all 265 pairs:
2.753)
Matchmaker modeller_multitemplate_1.pdb, chain C (#10) with 7smm, chain B
(#9), sequence alignment score = 437.8
RMSD between 170 pruned atom pairs is 1.180 angstroms; (across all 294 pairs:
6.650)
> show #!4 models
> view
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #11 to #10/A & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker modeller_multitemplate_1.pdb, chain A (#10) with
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb,
chain A (#11), sequence alignment score = 672.1
RMSD between 129 pruned atom pairs is 0.719 angstroms; (across all 133 pairs:
1.671)
> color #11 #ff2f92ff
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
Chain information for
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
#12
---
Chain | Description
A | No description available
> select add #10
20213 atoms, 12891 bonds, 4 pseudobonds, 2361 residues, 4 models selected
> select add #11
23070 atoms, 17978 bonds, 4 pseudobonds, 2539 residues, 4 models selected
> select subtract #10
10515 atoms, 5087 bonds, 4 pseudobonds, 979 residues, 3 models selected
> select subtract #11
5496 atoms, 4 pseudobonds, 667 residues, 2 models selected
> select add #4
14348 atoms, 14751 bonds, 5 pseudobonds, 1729 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #12
5019 atoms, 5087 bonds, 312 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 312 residues changed
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #12 to #10/B & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker modeller_multitemplate_1.pdb, chain B (#10) with
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb,
chain B (#12), sequence alignment score = 606.5
RMSD between 103 pruned atom pairs is 1.140 angstroms; (across all 125 pairs:
4.292)
> ui tool show Matchmaker
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
Chain information for
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
#13
---
Chain | Description
A | No description available
> select add #4
23001 atoms, 14751 bonds, 5 pseudobonds, 2575 residues, 5 models selected
> select subtract #4
8653 atoms, 846 residues, 3 models selected
> hide #!4 models
> select add #10
16373 atoms, 12891 bonds, 1798 residues, 3 models selected
> select add #11
19359 atoms, 17978 bonds, 1984 residues, 3 models selected
> select subtract #10
6804 atoms, 5087 bonds, 424 residues, 2 models selected
> select subtract #11
1785 atoms, 112 residues, 1 model selected
> select add #12
5019 atoms, 5087 bonds, 312 residues, 1 model selected
> select add #13
10038 atoms, 10174 bonds, 624 residues, 2 models selected
> select subtract #12
5019 atoms, 5087 bonds, 312 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 312 residues changed
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
Chain information for
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
#14
---
Chain | Description
A | No description available
> select subtract #13
Nothing selected
> select add #14
5019 atoms, 5087 bonds, 312 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel D
Chain IDs of 312 residues changed
> open /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
Chain information for
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb
#15
---
Chain | Description
A | No description available
> select subtract #14
Nothing selected
> select add #15
5019 atoms, 5087 bonds, 312 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel E
Chain IDs of 312 residues changed
> view
> ui tool show Matchmaker
[Repeated 2 time(s)]
> matchmaker #11 to #10/A & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker modeller_multitemplate_1.pdb, chain A (#10) with
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb,
chain A (#11), sequence alignment score = 653.5
RMSD between 124 pruned atom pairs is 0.692 angstroms; (across all 129 pairs:
1.697)
> ui tool show Matchmaker
> matchmaker #12 to #10/B & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker modeller_multitemplate_1.pdb, chain B (#10) with
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb,
chain B (#12), sequence alignment score = 619.2
RMSD between 103 pruned atom pairs is 1.131 angstroms; (across all 128 pairs:
4.248)
> ui tool show Matchmaker
> matchmaker #13 to #10/C & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker modeller_multitemplate_1.pdb, chain C (#10) with
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb,
chain C (#13), sequence alignment score = 580.6
RMSD between 96 pruned atom pairs is 1.168 angstroms; (across all 116 pairs:
3.868)
> ui tool show Matchmaker
> matchmaker #14 to #10/D & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker modeller_multitemplate_1.pdb, chain D (#10) with
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb,
chain D (#14), sequence alignment score = 582.2
RMSD between 100 pruned atom pairs is 1.150 angstroms; (across all 117 pairs:
3.332)
> ui tool show Matchmaker
> matchmaker #15 to #10/E & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker modeller_multitemplate_1.pdb, chain E (#10) with
Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_4_Monomer.pdb,
chain E (#15), sequence alignment score = 618.5
RMSD between 101 pruned atom pairs is 1.119 angstroms; (across all 126 pairs:
3.576)
> color #12 #ff2f92ff
> color #13 #ff2f92ff
> color #14 #ff2f92ff
> color #15 #ff2f92ff
> hide #10 models
> save /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/ChimeraX-
> ModellerComparative/Modeller_ChainAOfAllRestingStates_4AlphaFold_Bottom+TopMatched_5_HomoMonomer.cxs
Taking snapshot of stepper: modeller_multitemplate_1.pdb
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 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1392, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
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 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7f8902493b50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f84655373a0>
'modeller_multitemplate_1.pdb'
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: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f8902493b50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f84655373a0>
'modeller_multitemplate_1.pdb': Error while saving session data for 'isolde
residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper object at
0x7f8902493b50> -> <chimerax.atomic.structure.AtomicStructure object at
0x7f84655373a0> 'modeller_multitemplate_1.pdb'
ValueError: error processing: 'isolde residue stepper 0' -> ->
'modeller_multitemplate_1.pdb': Error while saving session data for 'isolde
residue stepper 0' -> -> 'modeller_multitemplate_1.pdb'
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 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1392, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 344, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
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 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7f8902493b50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f84655373a0>
'modeller_multitemplate_1.pdb'
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: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f8902493b50> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f84655373a0>
'modeller_multitemplate_1.pdb': Error while saving session data for 'isolde
residue stepper 0' -> <chimerax.isolde.navigate.ResidueStepper object at
0x7f8902493b50> -> <chimerax.atomic.structure.AtomicStructure object at
0x7f84655373a0> 'modeller_multitemplate_1.pdb'
ValueError: error processing: 'isolde residue stepper 0' -> ->
'modeller_multitemplate_1.pdb': Error while saving session data for 'isolde
residue stepper 0' -> -> 'modeller_multitemplate_1.pdb'
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.
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: 4 days, 23 hours, 27 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-PDBImages: 1.1
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-QScore: 1.0
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-StarMap: 1.2.15
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
pyqtgraph: 0.13.3
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
Send2Trash: 1.8.2
SEQCROW: 1.7.3
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 (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE ResidueStepper holding reference to dead structure |
comment:2 by , 19 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Sorry it's taken such a ridiculously long time, but this will be fixed in the next release. See #14894 if you're interested in the gory details.
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Reported by Jason Held