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Opened 9 months ago
Closed 9 months ago
#16849 closed defect (duplicate)
'AtomicStructure' object has no attribute '_alt_loc_changes_handler'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:\Users\fbumb\OneDrive\MIPS\papers\Survodutide\GLP-1R\20250212_GLP-!R_all_sidechain_analysis.cxs
> format session
Log from Wed Feb 12 19:19:19 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N-
> term.cxs
Log from Mon Feb 10 11:08:48 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:\Users\fbumb\OneDrive\MIPS\papers\Survodutide\GLP-1R\TM_aligned\sidechains_individual\20250120_GLP-1R_Surv_sidechains_TM4-5_N-
> term.cxs format session
Log from Mon Feb 10 10:48:48 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N-
> term.cxs
Log from Wed Jan 29 12:36:00 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_GCG_sidechains_TM4-5_N-
> term.cxs
Log from Mon Jan 20 12:03:19 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
Log from Mon Nov 18 14:28:29 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
Log from Tue Oct 15 08:56:43 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
Log from Mon Oct 14 14:03:14 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_bottom.cxs
Log from Wed Oct 9 12:11:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:\Users\fbumb\OneDrive\MIPS\papers\Survodutide\GLP-1R\20241008_GLP-1R_GLP-1_sidechains_TM4-5_bottom.cxs
> format session
Log from Wed Oct 9 11:31:24 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_Surv_sidechains_TM4-5_bottom.cxs
Log from Tue Oct 8 16:46:02 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241007_GLP-1R_all.cxs
Log from Mon Oct 7 16:36:45 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
Log from Fri Oct 4 18:32:41 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
Log from Fri Oct 4 15:19:48 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
Log from Fri Oct 4 12:33:42 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/pdb/GLP-1R_BI456906/GLP1_BI456906_20240906_revised.pdb
Chain information for GLP1_BI456906_20240906_revised.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide atoms
> show cartoons
> ui tool show "Color Actions"
> set bgColor white
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/6x18_GLP-1R_GLP-1_Gs.pdb
6x18_GLP-1R_GLP-1_Gs.pdb title:
GLP-1 peptide hormone bound to glucagon-like peptide-1 (GLP-1) receptor [more
info...]
Chain information for 6x18_GLP-1R_GLP-1_Gs.pdb #2
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394
B | transducin β chain 1 | GBB1_HUMAN 2-340
G | G γ-I | GBG2_HUMAN 5-62
N | NANOBODY35 |
P | GLP-1 peptide hormone | GLUC_HUMAN 7-36
R | GLP-1R | GLP1R_HUMAN 24-463
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #!2 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1901.3
RMSD between 349 pruned atom pairs is 1.013 angstroms; (across all 378 pairs:
1.559)
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/GLP1R_GCG-
> PublicationFINAL_MattB_25012024.pdb
Chain information for GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb #3
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide atoms
> show cartoons
> matchmaker #!3 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP1R_GCG-
PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence alignment score =
1874.9
RMSD between 306 pruned atom pairs is 0.870 angstroms; (across all 378 pairs:
1.999)
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb
Chain information for Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb #4
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide atoms
> show cartoons
> matchmaker #!4 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence
alignment score = 1945.1
RMSD between 325 pruned atom pairs is 1.204 angstroms; (across all 378 pairs:
1.694)
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/P15_GLP1R_PublicationFINAL_MattB_25012024.pdb
Chain information for P15_GLP1R_PublicationFINAL_MattB_25012024.pdb #5
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide atoms
> show cartoons
> matchmaker #!5 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence
alignment score = 1873.4
RMSD between 338 pruned atom pairs is 0.880 angstroms; (across all 371 pairs:
1.535)
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/7vbh_P20_GLP-1R_GsiN18.pdb
7vbh_P20_GLP-1R_GsiN18.pdb title:
Cryo-em structure of the gipr/GLP-1R/GCGR triagonist peptide 20-bound human
GLP-1R-GS complex [more info...]
Chain information for 7vbh_P20_GLP-1R_GsiN18.pdb #6
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394
B | transducin β chain 1 | GBB1_RAT 2-340
G | G γ-I | GBG2_BOVIN 2-71
N | nanobody 35 |
P | peptide 20 |
R | glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463
Non-standard residues in 7vbh_P20_GLP-1R_GsiN18.pdb #6
---
AIB — α-aminoisobutyric acid
D6M — N-hexadecanoyl-L-glutamic acid
> hide atoms
> show cartoons
> matchmaker #!6 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1868.3
RMSD between 265 pruned atom pairs is 0.836 angstroms; (across all 378 pairs:
2.278)
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/8jip_MEDI0382_GLP-1R_Gs.pdb
8jip_MEDI0382_GLP-1R_Gs.pdb title:
Cryo-em structure of the GLP-1R/GCGR dual agonist MEDI0382-bound human
GLP-1R-GS complex [more info...]
Chain information for 8jip_MEDI0382_GLP-1R_Gs.pdb #7
---
Chain | Description | UniProt
A | guanine nucleotide-binding protein G(S) subunit α isoforms short |
B | transducin β chain 1 | GBB1_RAT 2-340
G | G γ-I | GBG2_BOVIN 2-71
N | nanobody 35 |
P | MEDI0382 |
R | glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463
Non-standard residues in 8jip_MEDI0382_GLP-1R_Gs.pdb #7
---
D6M — N-hexadecanoyl-L-glutamic acid
> hide atoms
> show cartoons
> matchmaker #!7 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1842.5
RMSD between 307 pruned atom pairs is 0.972 angstroms; (across all 376 pairs:
1.711)
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/8jir_SAR425899_GLP-1R_Gs.pdb
8jir_SAR425899_GLP-1R_Gs.pdb title:
Cryo-em structure of the GLP-1R/GCGR dual agonist SAR425899-bound human
GLP-1R-GS complex [more info...]
Chain information for 8jir_SAR425899_GLP-1R_Gs.pdb #8
---
Chain | Description | UniProt
A | guanine nucleotide-binding protein G(S) subunit α isoforms short |
B | transducin β chain 1 | GBB1_RAT 2-340
G | G γ-I | GBG2_BOVIN 2-71
N | nanobody 35 |
P | SAR425899 |
R | glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463
Non-standard residues in 8jir_SAR425899_GLP-1R_Gs.pdb #8
---
D6M — N-hexadecanoyl-L-glutamic acid
> hide atoms
> show cartoons
> matchmaker #!8 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1839.5
RMSD between 292 pruned atom pairs is 0.888 angstroms; (across all 376 pairs:
2.073)
> dssp
> cartoon style helix width 1.0 thickness 0.2
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show Matchmaker
> select #1/R
2919 atoms, 3011 bonds, 2 pseudobonds, 378 residues, 2 models selected
> color (#!1 & sel) forest green
> select #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> color sel hot pink
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> dssp
> show #!2 models
> select #1/R
2919 atoms, 3011 bonds, 2 pseudobonds, 378 residues, 2 models selected
> color (#!1 & sel) hot pink
> select #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> select #1/R
2919 atoms, 3011 bonds, 2 pseudobonds, 378 residues, 2 models selected
> ui tool show "Color Actions"
> set bgColor #ffaaffff
> set bgColor #ffffffff
No target buttons for the coloring action are checked
[Repeated 30 time(s)]
> color sel plum target c
> color sel plum target ac
> select #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> color sel deep sky blue target ac
> color sel cyan target ac
> color sel cornflower blue target ac
> color sel powder blue target ac
> color sel light sky blue target ac
> color sel sky blue target ac
> color sel light sky blue target ac
> color sel sky blue target ac
> select #2/R
3158 atoms, 3239 bonds, 2 pseudobonds, 404 residues, 2 models selected
> color sel medium sea green target ac
> color sel forest green target ac
> color sel dark sea green target ac
> color sel medium sea green target ac
> select #2/P
238 atoms, 238 bonds, 35 residues, 1 model selected
> color sel tomato target ac
> color sel coral target ac
> color sel light coral target ac
> select clear
> show #!3 models
> select #3/R
5476 atoms, 5555 bonds, 2 pseudobonds, 381 residues, 2 models selected
> color sel steel blue target ac
> select #3/P
470 atoms, 476 bonds, 29 residues, 1 model selected
> color sel rosy brown target ac
> color sel khaki target ac
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> select #4/R
3129 atoms, 3231 bonds, 2 pseudobonds, 384 residues, 2 models selected
> color sel goldenrod target ac
> color sel dark green target ac
> color sel goldenrod target ac
> select #4/P
245 atoms, 251 bonds, 29 residues, 1 model selected
> color sel silver target ac
> color sel dark gray target ac
> select clear
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/R
3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected
> color sel olive drab target ac
[Repeated 1 time(s)]
> color sel brown target ac
[Repeated 1 time(s)]
> color sel olive target ac
[Repeated 1 time(s)]
> color sel sea green target ac
[Repeated 1 time(s)]
> color sel medium blue target ac
> color sel royal blue target ac
> color sel dodger blue target ac
[Repeated 1 time(s)]
> color sel blue target ac
> select #5/P
231 atoms, 237 bonds, 28 residues, 1 model selected
> color sel pale green target ac
> color sel turquoise target ac
> color sel medium aquamarine target ac
> color sel chartreuse target ac
> color sel lime green target ac
> color sel light green target ac
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> select #6/R
3105 atoms, 3204 bonds, 2 pseudobonds, 382 residues, 2 models selected
> color sel blue violet target ac
> color sel rebecca purple target ac
> color sel blue violet target ac
> color sel dark orchid target ac
> color sel dark magenta target ac
> color sel purple target ac
[Repeated 1 time(s)]
> color sel dark magenta target ac
> color sel purple target ac
> color sel dark magenta target ac
> color sel purple target ac
> select #6/P
262 atoms, 267 bonds, 30 residues, 1 model selected
> color sel dark olive green target ac
> color sel olive drab target ac
> select clear
> show #!7 models
> select #7/R
3109 atoms, 3207 bonds, 1 pseudobond, 386 residues, 2 models selected
> color sel maroon target ac
> select #7/P
294 atoms, 298 bonds, 30 residues, 1 model selected
> color sel cadet blue target ac
> color sel thistle target ac
[Repeated 1 time(s)]
> color sel light steel blue target ac
[Repeated 1 time(s)]
> color sel medium spring green target ac
> color sel lime target ac
> color sel yellow green target ac
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8/R
2886 atoms, 2964 bonds, 1 pseudobond, 383 residues, 2 models selected
> color sel coral target ac
> color sel orange target ac
> color sel dark orange target ac
> color sel green yellow target ac
> color sel lime target ac
> color sel light coral target ac
> color sel orange red target ac
> select #8/P
252 atoms, 256 bonds, 30 residues, 1 model selected
> color sel medium purple target ac
> select clear
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!3 models
> hide #!5 models
> hide #!4 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> select #8/P
252 atoms, 256 bonds, 30 residues, 1 model selected
> color sel dark orchid target ac
> select clear
> show #!6 models
> hide #!8 models
> select #6/R
3105 atoms, 3204 bonds, 2 pseudobonds, 382 residues, 2 models selected
> color sel rebecca purple target ac
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
> log metadata #3
No models had metadata
> log chains #3
Chain information for GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb #3
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> log metadata #3
No models had metadata
> log chains #3
Chain information for GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb #3
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> log metadata #3
No models had metadata
> log chains #3
Chain information for GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb #3
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> view #3 clip false
No displayed objects specified.
> color #3 #b42b8bff
> undo
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!5 models
> show #!4 models
> show #!7 models
> show #!8 models
> show #!4 target m
[Repeated 1 time(s)]
> view #4 clip false
[Repeated 1 time(s)]
> show #!4 target m
> view #4 clip false
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
> ui tool show "Color Actions"
> select #1/R
2919 atoms, 3011 bonds, 2 pseudobonds, 378 residues, 2 models selected
> select #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> ui tool show "Color Actions"
> select add #1
9028 atoms, 9234 bonds, 4 pseudobonds, 1169 residues, 2 models selected
> select subtract #1.1
9028 atoms, 9234 bonds, 1169 residues, 1 model selected
> select add #1
9028 atoms, 9234 bonds, 4 pseudobonds, 1169 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #1.1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> select #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> log metadata #6
Metadata for 7vbh_P20_GLP-1R_GsiN18.pdb #6
---
Title | Cryo-em structure of the gipr/GLP-1R/GCGR triagonist peptide 20-bound human GLP-1R-GS complex
Citation | Structural insights INTO multiplexed pharmacological actionsof tirzepatide and peptide 20 At the gip, GLP-1 or glucagonreceptors. PMID: 35217653
Non-standard residues | AIB — α-aminoisobutyric acid
D6M — N-hexadecanoyl-L-glutamic acid
Gene sources | Homo sapiens (human)
Homo sapiens (human)
Homo sapiens (human)
Homo sapiens (human)
Homo sapiens (human)
Experimental method | Electron microscopy
Resolution | 3.00Å
> log chains #6
Chain information for 7vbh_P20_GLP-1R_GsiN18.pdb #6
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394
B | transducin β chain 1 | GBB1_RAT 2-340
G | G γ-I | GBG2_BOVIN 2-71
N | nanobody 35 |
P | peptide 20 |
R | glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463
> ui tool show "Color Actions"
> show #!1 target m
[Repeated 1 time(s)]
> view #1 clip false
[Repeated 1 time(s)]
> log metadata #1
No models had metadata
> log chains #1
Chain information for GLP1_BI456906_20240906_revised.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> ui tool show "Selection Inspector"
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> show #!2 models
> ui tool show "Selection Inspector"
> select #2/R
3158 atoms, 3239 bonds, 2 pseudobonds, 404 residues, 2 models selected
> ui tool show "Selection Inspector"
> select #2/P
238 atoms, 238 bonds, 35 residues, 1 model selected
> hide #!2 models
> show #!3 models
> select #3/R
5476 atoms, 5555 bonds, 2 pseudobonds, 381 residues, 2 models selected
> select #3/P
470 atoms, 476 bonds, 29 residues, 1 model selected
> show #!4 models
> hide #!3 models
> select #4/R
3129 atoms, 3231 bonds, 2 pseudobonds, 384 residues, 2 models selected
> select #4/P
245 atoms, 251 bonds, 29 residues, 1 model selected
> hide #!4 models
> show #!5 models
> select #5/R
3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected
> color sel #0055ff atoms
> ui tool show "Color Actions"
> color sel medium blue target ac
> color sel royal blue target ac
> color sel navy target ac
> color sel medium blue target ac
> color sel blue target ac
> color sel royal blue target ac
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> color (#!5 & sel) #5500ffff
> color (#!5 & sel) #00aaffff
> color (#!5 & sel) #11d3ffff
> color (#!5 & sel) #11cbffff
> color (#!5 & sel) #13c8ffff
> color (#!5 & sel) #18baffff
> color (#!5 & sel) #19baffff
> color (#!5 & sel) #1abaffff
> color (#!5 & sel) #1cbbffff
> color (#!5 & sel) #1dbbffff
> color (#!5 & sel) #22bdffff
> color (#!5 & sel) #26beffff
> color (#!5 & sel) #2abfffff
> color (#!5 & sel) #2bbcffff
> color (#!5 & sel) #31beffff
> color (#!5 & sel) #35bfffff
> color (#!5 & sel) #38b9ffff
> color (#!5 & sel) #3ab3ffff
> color (#!5 & sel) #3cb4ffff
> color (#!5 & sel) #3eb2ffff
> color (#!5 & sel) #43aeffff
> color (#!5 & sel) #47a6ffff
> color (#!5 & sel) #47a0ffff
> color (#!5 & sel) #479affff
> color (#!5 & sel) #4791ffff
> color (#!5 & sel) #4687ffff
> color (#!5 & sel) #457dffff
> color (#!5 & sel) #4164ffff
> color (#!5 & sel) #3e58ffff
> color (#!5 & sel) #3e51ffff
> color (#!5 & sel) #3e4bffff
> color (#!5 & sel) #3e51ffff
> color (#!5 & sel) #3e61ffff
> color (#!5 & sel) #3e71ffff
> color (#!5 & sel) #407cffff
> color (#!5 & sel) #418affff
> color (#!5 & sel) #4394ffff
> color (#!5 & sel) #43a7ffff
> color (#!5 & sel) #43bdffff
> color (#!5 & sel) #43c7ffff
> color (#!5 & sel) #43cdffff
> color (#!5 & sel) #43d3ffff
> color (#!5 & sel) #46d7ffff
> color (#!5 & sel) #49e1ffff
> color (#!5 & sel) #49e7ffff
> color (#!5 & sel) #49e1ffff
> color (#!5 & sel) #47ddffff
> color (#!5 & sel) #46ddffff
> color (#!5 & sel) #41ecffff
> color (#!5 & sel) #35ebffff
> color (#!5 & sel) #30eaffff
> color (#!5 & sel) #2eeaffff
> color (#!5 & sel) #2aeaffff
> color (#!5 & sel) #2beaffff
> color (#!5 & sel) #43d6ffff
> color (#!5 & sel) #5cc6ffff
> color (#!5 & sel) #63c3ffff
> color (#!5 & sel) #67c5ffff
> color (#!5 & sel) #6ac6ffff
> color (#!5 & sel) #6cc7ffff
> color (#!5 & sel) #75caffff
> color (#!5 & sel) #7ccbffff
> color (#!5 & sel) #7dcbffff
> color (#!5 & sel) #7dc7ffff
> color (#!5 & sel) #77b2ffff
> color (#!5 & sel) #74acffff
> color (#!5 & sel) #74a5ffff
> color (#!5 & sel) #74a0ffff
> color (#!5 & sel) #749effff
> color (#!5 & sel) #7499ffff
> color (#!5 & sel) #7494ffff
> color (#!5 & sel) #7394ffff
> color (#!5 & sel) #7091ffff
> color (#!5 & sel) #6f95ffff
> color (#!5 & sel) #7091ffff
> color (#!5 & sel) #7494ffff
> color (#!5 & sel) #7595ffff
> color (#!5 & sel) #7998ffff
> color (#!5 & sel) #7b9affff
> color (#!5 & sel) #7d99ffff
> color (#!5 & sel) #809cffff
> color (#!5 & sel) #819cffff
> color (#!5 & sel) #87a1ffff
> color (#!5 & sel) #89a3ffff
> color (#!5 & sel) #8ba4ffff
> color (#!5 & sel) #8baaffff
> color (#!5 & sel) #8baeffff
> color (#!5 & sel) #8aafffff
> color (#!5 & sel) #8ab3ffff
> color (#!5 & sel) #89b2ffff
> color (#!5 & sel) #89b6ffff
> color (#!5 & sel) #89b8ffff
> color (#!5 & sel) #89bcffff
> color (#!5 & sel) #89beffff
> color (#!5 & sel) #89c2ffff
> color (#!5 & sel) #89c6ffff
> color (#!5 & sel) #87cbffff
> color (#!5 & sel) #87d1ffff
> color (#!5 & sel) #87dbffff
> color (#!5 & sel) #89e5ffff
> color (#!5 & sel) #8aefffff
> color (#!5 & sel) #8bffffff
> color (#!5 & sel) #8efff2ff
> color (#!5 & sel) #8effecff
> color (#!5 & sel) #8effe7ff
> color (#!5 & sel) #8effe8ff
> color (#!5 & sel) #8efff6ff
> color (#!5 & sel) #8efdffff
> color (#!5 & sel) #8fe5ffff
> color (#!5 & sel) #8fb2ffff
> color (#!5 & sel) #9f92ffff
> color (#!5 & sel) #c194ffff
> color (#!5 & sel) #cd94ffff
> color (#!5 & sel) #d294ffff
> color (#!5 & sel) #db94ffff
> color (#!5 & sel) #df94ffff
> color (#!5 & sel) #ed92ffff
> color (#!5 & sel) #e38fffff
> color (#!5 & sel) #b686ffff
> color (#!5 & sel) #75ffacff
> color (#!5 & sel) #74ffacff
> color (#!5 & sel) #6cffb6ff
> color (#!5 & sel) #69ffd5ff
> color (#!5 & sel) #66c4ffff
> color (#!5 & sel) #67a9ffff
> color (#!5 & sel) #6a8dffff
> color (#!5 & sel) #6a8affff
> color (#!5 & sel) #6b86ffff
> color (#!5 & sel) #6b81ffff
> color (#!5 & sel) #6b75ffff
> color (#!5 & sel) #856fffff
> color (#!5 & sel) #9572ffff
> color (#!5 & sel) #9470ffff
> color (#!5 & sel) #9970ffff
> color (#!5 & sel) #9d70ffff
> color (#!5 & sel) #a970ffff
> color (#!5 & sel) #aa72ffff
> color (#!5 & sel) #af79ffff
> color (#!5 & sel) #b17dffff
> color (#!5 & sel) #ac7cffff
> color (#!5 & sel) #8069ffff
> color (#!5 & sel) #6b60ffff
> color (#!5 & sel) #695effff
> color (#!5 & sel) #6661ffff
> color (#!5 & sel) #6a65ffff
> color (#!5 & sel) #7c77ffff
> color (#!5 & sel) #8b80ffff
> color (#!5 & sel) #9d90ffff
> color (#!5 & sel) #af9bffff
> color (#!5 & sel) #b69effff
> color (#!5 & sel) #c1a2ffff
> color (#!5 & sel) #c4a2ffff
> color (#!5 & sel) #cca7ffff
> color (#!5 & sel) #cda9ffff
> color (#!5 & sel) #d0a9ffff
> color (#!5 & sel) #d4aeffff
> color (#!5 & sel) #d4afffff
> color (#!5 & sel) #d5b0ffff
> color (#!5 & sel) #d6b2ffff
> color (#!5 & sel) #dab4ffff
> color (#!5 & sel) #dab5ffff
> color (#!5 & sel) #dcb5ffff
> color (#!5 & sel) #ddb7ffff
> color (#!5 & sel) #deb9ffff
> color (#!5 & sel) #e1bcffff
> color (#!5 & sel) #e5c0ffff
> color (#!5 & sel) #eec7ffff
> color (#!5 & sel) #edc2ffff
> color (#!5 & sel) #e39cffff
> color (#!5 & sel) #d677ffff
> color (#!5 & sel) #c560ffff
> color (#!5 & sel) #c35cffff
> color (#!5 & sel) #c155ffff
> color (#!5 & sel) #c053ffff
> color (#!5 & sel) #b949ffff
> color (#!5 & sel) #952bffff
> color (#!5 & sel) #851affff
> color (#!5 & sel) #7e14ffff
> color (#!5 & sel) #5c11ffff
> color (#!5 & sel) #4911ffff
> color (#!5 & sel) #4111ffff
> color (#!5 & sel) #1323ffff
> color (#!5 & sel) #1332ffff
> color (#!5 & sel) #1336ffff
> color (#!5 & sel) #1371ffff
> color (#!5 & sel) #138dffff
> color (#!5 & sel) #1391ffff
> color (#!5 & sel) #1399ffff
> color (#!5 & sel) #13a1ffff
> color (#!5 & sel) #00aaffff
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> color #5 #00699eff
> color #5 #00aaffff
> color #5 #aaaa7fff
> undo
> select #5/P
231 atoms, 237 bonds, 28 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lawn green target ac
> color sel green yellow target ac
> color sel light green target ac
> select #5/R
3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected
> color sel burly wood target ac
> color sel rosy brown target ac
> color sel light steel blue target ac
> select #5/P
231 atoms, 237 bonds, 28 residues, 1 model selected
> color sel olive drab target ac
> select clear
> select #5/R
3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected
> color sel steel blue target ac
> color sel deep sky blue target ac
> color sel royal blue target ac
> select clear
> hide #!5 models
> show #!3 models
> show #!5 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> show #!4 models
> show #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!1 models
> select #3/R
5476 atoms, 5555 bonds, 2 pseudobonds, 381 residues, 2 models selected
> color sel dark cyan target ac
> color sel cadet blue target ac
> color sel medium turquoise target ac
> color sel light sea green target ac
> color sel medium sea green target ac
> color sel dark olive green target ac
> color sel dark sea green target ac
> color sel sea green target ac
> color sel teal target ac
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> select clear
> show #!2 models
> select #2/R
3158 atoms, 3239 bonds, 2 pseudobonds, 404 residues, 2 models selected
> color sel forest green target ac
> color sel lime green target ac
> color sel pale green target ac
> color sel light green target ac
> color sel aquamarine target ac
> color sel medium spring green target ac
> select clear
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> select #2/R
3158 atoms, 3239 bonds, 2 pseudobonds, 404 residues, 2 models selected
> select #2/P
238 atoms, 238 bonds, 35 residues, 1 model selected
> select #3/R
5476 atoms, 5555 bonds, 2 pseudobonds, 381 residues, 2 models selected
> select #3/P
470 atoms, 476 bonds, 29 residues, 1 model selected
> select #4/R
3129 atoms, 3231 bonds, 2 pseudobonds, 384 residues, 2 models selected
> select #4/P
245 atoms, 251 bonds, 29 residues, 1 model selected
> show #!5 models
> select #5/R
3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected
> select #5/P
231 atoms, 237 bonds, 28 residues, 1 model selected
> hide #!5 models
> show #!6 models
> select #6/R
3105 atoms, 3204 bonds, 2 pseudobonds, 382 residues, 2 models selected
> select #6/P
262 atoms, 267 bonds, 30 residues, 1 model selected
> hide #!6 models
> show #!7 models
> select #7/R
3109 atoms, 3207 bonds, 1 pseudobond, 386 residues, 2 models selected
> select #7/P
294 atoms, 298 bonds, 30 residues, 1 model selected
> hide #!7 models
> show #!8 models
> show #!7 models
> hide #!7 models
> select #8/R
2886 atoms, 2964 bonds, 1 pseudobond, 383 residues, 2 models selected
> select #8/P
252 atoms, 256 bonds, 30 residues, 1 model selected
> select clear
> hide #!8 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
——— End of log from Fri Oct 4 12:33:42 2024 ———
opened ChimeraX session
> cartoon style helix width 1.5 thickness 0.5
> show #!8 models
> hide #!1 models
> lighting simple
[Repeated 1 time(s)]
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> select #8/R
2886 atoms, 2964 bonds, 1 pseudobond, 383 residues, 2 models selected
> color (#!8 & sel) #ff8c00ff
> select clear
> hide #!8 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!5 models
> select #5/P
231 atoms, 237 bonds, 28 residues, 1 model selected
> color sel #aa5500ff
> select clear
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!3 models
> show #!1 models
> hide #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
> select add #1/A#3/A#4/A#5/A
7643 atoms, 7785 bonds, 9 pseudobonds, 929 residues, 8 models selected
> select add #1/B#3/B#4/B#5/B
18046 atoms, 18376 bonds, 9 pseudobonds, 2283 residues, 8 models selected
> select add #1/G#3/G#4/G#5/G
19764 atoms, 20118 bonds, 9 pseudobonds, 2510 residues, 8 models selected
> select add #1/G#3/G#4/G#5/G
19764 atoms, 20118 bonds, 9 pseudobonds, 2510 residues, 8 models selected
> select add #2/G#6/G#7/G#8/G
21502 atoms, 21880 bonds, 9 pseudobonds, 2737 residues, 12 models selected
> select add #1/N#3/N#4/N#5/N
25367 atoms, 25833 bonds, 9 pseudobonds, 3245 residues, 12 models selected
> select add #2/N
26333 atoms, 26816 bonds, 9 pseudobonds, 3376 residues, 12 models selected
> select add #2/A#6/A
31040 atoms, 31591 bonds, 14 pseudobonds, 3965 residues, 14 models selected
> select add #7/A#8/A
34940 atoms, 35567 bonds, 16 pseudobonds, 4439 residues, 16 models selected
> select add #6/N#7/N#8/N
37829 atoms, 38521 bonds, 16 pseudobonds, 4819 residues, 16 models selected
> select add #2/B#6/B#7/B#8/B
48235 atoms, 49071 bonds, 16 pseudobonds, 6216 residues, 16 models selected
> hide sel & #!1 cartoons
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!6 models
> show #!5 models
> show #!7 models
> show #!8 models
> hide sel cartoons
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_GLP-1_helix_overview.png
> width 2000 height 1448 supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_GCG_helix_overview.png
> width 2000 height 1448 supersample 4 transparentBackground true
> hide #!3 models
> show #!4 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_Oxyn_helix_overview.png
> width 2000 height 1448 supersample 4 transparentBackground true
> hide #!4 models
> show #!5 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_P15_helix_overview.png
> width 2000 height 1448 supersample 4 transparentBackground true
> hide #!5 models
> show #!6 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_P20_helix_overview.png
> width 2000 height 1448 supersample 4 transparentBackground true
> hide #!6 models
> show #!7 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_MEDI_helix_overview.png
> width 2000 height 1448 supersample 4 transparentBackground true
> show #!8 models
> hide #!7 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_SAR_helix_overview.png
> width 2000 height 1448 supersample 4 transparentBackground true
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
——— End of log from Fri Oct 4 15:19:48 2024 ———
opened ChimeraX session
> hide #!8 models
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb
7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb title:
EX4-D-ala bound to the glucagon-like peptide-1 receptor/G protein complex
(conformer 1) [more info...]
Chain information for 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb #9
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394
B | transducin β chain 1 | GBB1_HUMAN 2-340
G | G γ-I | GBG2_HUMAN 5-62
N | NB35 |
P | EX4-D-ala |
R | GLP-1R | GLP1R_HUMAN 24-463
Non-standard residues in 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb #9
---
DAL — D-alanine
> select clear
> hide #!1,9 atoms
> select add #9
9160 atoms, 9368 bonds, 4 pseudobonds, 1169 residues, 2 models selected
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #!9 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment
score = 1869.5
RMSD between 291 pruned atom pairs is 0.846 angstroms; (across all 375 pairs:
1.874)
> select add #9/G
444 atoms, 450 bonds, 58 residues, 1 model selected
> select add #9/N
1417 atoms, 1445 bonds, 186 residues, 1 model selected
> select add #9/A
3346 atoms, 3410 bonds, 2 pseudobonds, 419 residues, 2 models selected
> select add #9/B
5961 atoms, 6072 bonds, 2 pseudobonds, 759 residues, 2 models selected
> hide sel cartoons
> select clear
> select add #9/P
236 atoms, 240 bonds, 29 residues, 1 model selected
> color sel #ff0000ff
> select clear
> select add #9/R
2963 atoms, 3056 bonds, 2 pseudobonds, 381 residues, 2 models selected
> color (#!9 & sel) #8fbc8fff
> select clear
> cartoon style helix width 1.5 thickness 0.5
> dssp
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs
——— End of log from Fri Oct 4 18:32:41 2024 ———
opened ChimeraX session
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/pdb/GLP-1R_BI6450/GLP-1R_BI6450_20240906_revised.pdb
Chain information for GLP-1R_BI6450_20240906_revised.pdb #10
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide #!1,9-10 atoms
> hide #!1 models
> hide #!9 models
> show #!10 cartoons
> cartoon style helix width 1.5 thickness 0.5
> dssp
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!10 to #1/R 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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score =
1935.5
RMSD between 355 pruned atom pairs is 0.861 angstroms; (across all 378 pairs:
1.141)
> select #10/R
2878 atoms, 2969 bonds, 2 pseudobonds, 378 residues, 2 models selected
> color (#!10 & sel) #9093c9ff
> select #10/P
231 atoms, 238 bonds, 28 residues, 1 model selected
> color sel #dd8ba7ff
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> select add #10/A
1844 atoms, 1879 bonds, 2 pseudobonds, 234 residues, 2 models selected
> select add #10/B
4418 atoms, 4500 bonds, 2 pseudobonds, 573 residues, 2 models selected
> select add #10/G
4792 atoms, 4880 bonds, 2 pseudobonds, 630 residues, 2 models selected
> select add #10/N
5756 atoms, 5866 bonds, 2 pseudobonds, 758 residues, 2 models selected
> hide sel cartoons
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241007_GLP-1R_all.cxs
> show #!6 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> hide #!1 models
> hide #!10 models
> show #!10 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241007_GLP-1R_all.cxs
——— End of log from Mon Oct 7 16:36:45 2024 ———
opened ChimeraX session
> show #!1 models
> hide #!10 models
> select /R:262-337
7015 atoms, 7225 bonds, 760 residues, 10 models selected
> hide sel & #!1 cartoons
> select #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 232 atom styles
> color sel byhetero
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true makePseudobonds false
> reveal true log true
[deleted to fit within ticket limits]
447 hydrogen bonds found
> select /R:299,300,310,306,298
559 atoms, 549 bonds, 50 residues, 10 models selected
> hide sel & #!1 atoms
> ribbon suppressBackboneDisplay false
> select /R:262-337
7015 atoms, 7225 bonds, 760 residues, 10 models selected
> hide sel & #!1 cartoons
> select up
7238 atoms, 7446 bonds, 786 residues, 10 models selected
> select /R:262-337
7015 atoms, 7225 bonds, 760 residues, 10 models selected
> select /R:29-32
241 atoms, 231 bonds, 36 residues, 10 models selected
> hide sel & #!1 cartoons
> select #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> hide sel cartoons
> select clear
> select /R:32
76 atoms, 66 bonds, 10 residues, 10 models selected
> show sel & #!1 cartoons
> select clear
> ui tool show "Side View"
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_Surv_sidechains_TM4-5_bottom.cxs
——— End of log from Tue Oct 8 16:46:02 2024 ———
opened ChimeraX session
> show #!2 models
> hide #!1 models
> select /R:262-337
7015 atoms, 7225 bonds, 760 residues, 10 models selected
> hide sel & #!2 cartoons
> show sel & #!2 cartoons
> hide sel & #!2 cartoons
> show #!1 models
> show sel & #!1-2 cartoons
> hide sel & #!1-2 cartoons
> hide #!1 models
> hide sel & #!2 atoms
> select clear
> hide #!2 atoms
> select #2/P
238 atoms, 238 bonds, 8 pseudobonds, 35 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> select add ::name="HOH"
375 atoms, 238 bonds, 116 pseudobonds, 172 residues, 8 models selected
> show sel & #!2 atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> style sel & #!2 stick
Changed 331 atom styles
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true makePseudobonds false
> reveal true log true
[deleted to fit within ticket limits]
450 hydrogen bonds found
> select clear
> style #!10 stick
Changed 8867 atom styles
> color #10 byhetero
> select /R:262-337
7015 atoms, 7225 bonds, 760 residues, 10 models selected
> hide sel & #!10 atoms
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_NLS_sidechains_TM4-5_bottom.cxs
> show #!1 models
> hide #!10 models
> hide #!1 models
> show #!2 models
> select /R:262-337
7015 atoms, 7225 bonds, 760 residues, 10 models selected
> hide sel & #!2 atoms
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> hide sel & #!4 atoms
> show #!5 models
> hide #!4 models
> hide sel & #!5 atoms
> hide #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!8 models
> hide #!7 models
> show #!9 models
> hide #!8 models
> show #!10 models
> hide #!9 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_bottom.cxs
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!10 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!9 models
> select add H
9249 atoms, 7225 bonds, 1095 residues, 10 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select clear
> select add #3/P
245 atoms, 251 bonds, 29 residues, 1 model selected
> select add ::name="HOH"
387 atoms, 251 bonds, 110 pseudobonds, 171 residues, 9 models selected
> show sel & #!3 atoms
> ui tool show H-Bonds
> hbonds sel color #000000 interModel false intraMol false intraRes false
> reveal true log true
[deleted to fit within ticket limits]
449 hydrogen bonds found
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_GCG_sidechains_TM4-5_bottom.cxs
> show #!10 models
> hide #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_bottom.cxs
> select /R:262-337
5716 atoms, 5905 bonds, 684 residues, 9 models selected
> hide sel & #!10 atoms
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_bottom.cxs
——— End of log from Wed Oct 9 12:11:44 2024 ———
opened ChimeraX session
> hide #!10 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide sel & #!2 atoms
> show #!3 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_Surv_TM4-5_bottom.png
> width 2000 height 1448 supersample 4 transparentBackground true
> hide #!1 models
> show #!2 models
> ui tool show "Side View"
> show #!1 models
> hide #!2 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_Surv_TM4-5_bottom.png
> width 2000 height 1448 supersample 4 transparentBackground true
> hide #!1 models
> show #!2 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GLP-1_TM4-5_bottom.png
> width 2000 height 1448 supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_bottom.png
> width 2000 height 1448 supersample 4 transparentBackground true
> show #!2 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> select /R:190,241
230 atoms, 220 bonds, 20 residues, 10 models selected
> show sel & #!1-3 atoms
> select clear
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select /R:233,371
160 atoms, 140 bonds, 20 residues, 10 models selected
> show #!2 models
> show #!3 models
> show sel & #!1-3 atoms
> select clear
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select /R:230
110 atoms, 110 bonds, 10 residues, 10 models selected
> show sel & #!1-3 atoms
> select /R:194
70 atoms, 60 bonds, 10 residues, 10 models selected
> show sel & #!1-3 atoms
> select /R:394
90 atoms, 80 bonds, 10 residues, 10 models selected
> show sel & #!1-3 atoms
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_Surv_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
> hide #!1 models
> show #!2 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GLP-1_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> show #!2 models
> select /R:364,367
200 atoms, 190 bonds, 20 residues, 10 models selected
> show sel & #!2-3 atoms
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> select clear
> show #!2 models
> select /R:187,367
220 atoms, 220 bonds, 20 residues, 10 models selected
> hide sel & #!2-3 atoms
> show #!1 models
> hide #!1 models
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> select /R:380
110 atoms, 100 bonds, 10 residues, 10 models selected
> hide sel & #!2 atoms
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GLP-1_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> show #!1 models
> hide #!3 models
> select /R:388
80 atoms, 70 bonds, 10 residues, 10 models selected
> show sel & #!1 atoms
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_Surv_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
——— End of log from Mon Oct 14 14:03:14 2024 ———
opened ChimeraX session
> select /R:197
90 atoms, 80 bonds, 10 residues, 10 models selected
> show sel & #!1 atoms
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
——— End of log from Tue Oct 15 08:56:43 2024 ———
opened ChimeraX session
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> mmaker #2-10 to #1/R:139-168,175-203,223-256,262-291,303-336,346-368,377-404
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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1066.6
RMSD between 208 pruned atom pairs is 0.530 angstroms; (across all 208 pairs:
0.530)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP1R_GCG-
PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence alignment score =
962.8
RMSD between 144 pruned atom pairs is 0.525 angstroms; (across all 144 pairs:
0.525)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence
alignment score = 1082
RMSD between 208 pruned atom pairs is 0.677 angstroms; (across all 208 pairs:
0.677)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence
alignment score = 1054
RMSD between 208 pruned atom pairs is 0.491 angstroms; (across all 208 pairs:
0.491)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1063
RMSD between 206 pruned atom pairs is 0.633 angstroms; (across all 208 pairs:
0.664)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1024
RMSD between 208 pruned atom pairs is 0.721 angstroms; (across all 208 pairs:
0.721)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1041.4
RMSD between 207 pruned atom pairs is 0.511 angstroms; (across all 208 pairs:
0.536)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment
score = 1070.8
RMSD between 208 pruned atom pairs is 0.458 angstroms; (across all 208 pairs:
0.458)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score =
1062.2
RMSD between 207 pruned atom pairs is 0.560 angstroms; (across all 208 pairs:
0.580)
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/20241008_GLP-1R_all_sidechains_TM4-5_N-
> term.cxs
——— End of log from Mon Nov 18 14:28:29 2024 ———
opened ChimeraX session
> mmaker #2-10 to #1/R:139-168,175-203,223-256,262-291,303-336,346-368,377-404
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 GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1066.6
RMSD between 208 pruned atom pairs is 0.530 angstroms; (across all 208 pairs:
0.530)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP1R_GCG-
PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence alignment score =
962.8
RMSD between 144 pruned atom pairs is 0.525 angstroms; (across all 144 pairs:
0.525)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence
alignment score = 1082
RMSD between 208 pruned atom pairs is 0.677 angstroms; (across all 208 pairs:
0.677)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence
alignment score = 1054
RMSD between 208 pruned atom pairs is 0.491 angstroms; (across all 208 pairs:
0.491)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1063
RMSD between 206 pruned atom pairs is 0.633 angstroms; (across all 208 pairs:
0.664)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1024
RMSD between 208 pruned atom pairs is 0.721 angstroms; (across all 208 pairs:
0.721)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1041.4
RMSD between 207 pruned atom pairs is 0.511 angstroms; (across all 208 pairs:
0.536)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment
score = 1070.8
RMSD between 208 pruned atom pairs is 0.458 angstroms; (across all 208 pairs:
0.458)
Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with
GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score =
1062.2
RMSD between 207 pruned atom pairs is 0.560 angstroms; (across all 208 pairs:
0.580)
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!1 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_GLP-1_sidechains_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_GLP-1_sidechains_TM4-5_N-
> term.cxs
> show #!3 models
> hide #!2 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_GCG_sidechains_TM4-5_N-
> term.cxs
——— End of log from Mon Jan 20 12:03:19 2025 ———
opened ChimeraX session
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> ui tool show H-Bonds
> hbonds sel color #434343 radius 0.08 interModel false intraMol false
> intraRes false reveal true log true
Atom specifier selects no atoms
> select /P
2466 atoms, 2515 bonds, 8 pseudobonds, 296 residues, 11 models selected
> hbonds sel color #434343 radius 0.08 interModel false intraMol false
> intraRes false reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R
PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N
[deleted to fit within ticket limits]
138 hydrogen bonds found
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> select clear
> hbonds reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R
PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N
72154 hydrogen bonds found
> hbonds intraModel false intraMol false intraRes false reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R
PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N
61828 hydrogen bonds found
> hbonds sel intraModel false intraMol false intraRes false reveal true
Atom specifier selects no atoms
> select /P
2466 atoms, 2515 bonds, 1796 pseudobonds, 296 residues, 11 models selected
> hbonds sel intraModel false intraMol false intraRes false reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R
PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N
2820 hydrogen bonds found
> hbonds sel interModel false intraMol false intraRes false reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R
PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N
138 hydrogen bonds found
> select add ::name="HOH"
2603 atoms, 2515 bonds, 36 pseudobonds, 433 residues, 12 models selected
> hbonds sel color #000000 interModel false intraMol false intraRes false
> reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R
PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N
544 hydrogen bonds found
> select clear
> ribbon suppressBackboneDisplay true
> select /R:337-425
6695 atoms, 6835 bonds, 8 pseudobonds, 815 residues, 18 models selected
> select /R:253-341
6475 atoms, 6676 bonds, 2 pseudobonds, 787 residues, 12 models selected
> hide sel & #!1 cartoons
> hide sel & #!1 atoms
> select clear
> select add #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/R:240@CG
1 atom, 1 residue, 1 model selected
> select #1/R:240
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:236
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:155
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:156
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/R:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:363@CG
1 atom, 1 residue, 1 model selected
> select #1/R:365
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:363@CG
1 atom, 1 residue, 1 model selected
> select #1/R:363@CG
1 atom, 1 residue, 1 model selected
> select #1/R:240
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:236
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #1/R:156
25 atoms, 23 bonds, 3 residues, 1 model selected
> select add #1/R:155
31 atoms, 28 bonds, 4 residues, 1 model selected
> select add #1/R:239
36 atoms, 32 bonds, 5 residues, 1 model selected
> select add #1/R:392
42 atoms, 37 bonds, 2 pseudobonds, 6 residues, 2 models selected
> select add #1/R:363@CG
43 atoms, 37 bonds, 2 pseudobonds, 7 residues, 2 models selected
> select add #1/R:389
49 atoms, 42 bonds, 2 pseudobonds, 8 residues, 2 models selected
> select add #1/R:386
56 atoms, 48 bonds, 2 pseudobonds, 9 residues, 2 models selected
> select add #1/R:145
68 atoms, 60 bonds, 2 pseudobonds, 10 residues, 2 models selected
> hide sel atoms
> select clear
> select #1/R:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/R:239
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/R:240
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:185
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/R:186
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/R:383
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:379
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:379
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:383
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /R:363,374
195 atoms, 194 bonds, 20 residues, 10 models selected
> hide sel & #!1 atoms
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N-
> term.cxs
——— End of log from Wed Jan 29 12:36:00 2025 ———
opened ChimeraX session
> close #1
> open
> C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/GLP1_BI456906_final_stubbed_checked_20250131.pdb
Chain information for GLP1_BI456906_final_stubbed_checked_20250131.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 atoms
> show #!1 cartoons
> dssp
> cartoon style helix width 1.5 thickness 0.5
> mmaker #2-10 to #1/R:139-168,175-203,223-256,262-291,303-336,346-368,377-404
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 GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1070.2
RMSD between 208 pruned atom pairs is 0.522 angstroms; (across all 208 pairs:
0.522)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence
alignment score = 962.8
RMSD between 144 pruned atom pairs is 0.528 angstroms; (across all 144 pairs:
0.528)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence
alignment score = 1085.6
RMSD between 208 pruned atom pairs is 0.656 angstroms; (across all 208 pairs:
0.656)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence
alignment score = 1057.6
RMSD between 208 pruned atom pairs is 0.490 angstroms; (across all 208 pairs:
0.490)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1066.6
RMSD between 206 pruned atom pairs is 0.633 angstroms; (across all 208 pairs:
0.664)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1027.6
RMSD between 208 pruned atom pairs is 0.706 angstroms; (across all 208 pairs:
0.706)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1045
RMSD between 206 pruned atom pairs is 0.484 angstroms; (across all 208 pairs:
0.531)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment
score = 1074.4
RMSD between 208 pruned atom pairs is 0.458 angstroms; (across all 208 pairs:
0.458)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with
GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score =
1065.8
RMSD between 207 pruned atom pairs is 0.552 angstroms; (across all 208 pairs:
0.573)
> select add #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true makePseudobonds false
> reveal true log true
[deleted to fit within ticket limits]
449 hydrogen bonds found
> select clear
> select add #1/R
2919 atoms, 3007 bonds, 2 pseudobonds, 378 residues, 2 models selected
> color (#!1 & sel) #dda0ddff
> select clear
> style #!1 stick
Changed 9031 atom styles
> color #1,11 byhetero
> select /R:253-341
6475 atoms, 6676 bonds, 2 pseudobonds, 787 residues, 12 models selected
> hide sel & #!1 cartoons
> hide sel & #!1 atoms
> select add #1/P
6707 atoms, 6915 bonds, 2 pseudobonds, 815 residues, 12 models selected
> hide sel & #!1 cartoons
> show sel & #!1 atoms
> select clear
> select /R:253-341
6475 atoms, 6676 bonds, 2 pseudobonds, 787 residues, 12 models selected
> hide sel & #!1 atoms
> select /R:190,198,380,388,371
457 atoms, 407 bonds, 50 residues, 10 models selected
> show sel & #!1 atoms
> select /R:190,198,380,388,371,149
527 atoms, 467 bonds, 60 residues, 10 models selected
> show sel & #!1 atoms
> select clear
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Ex4_sidechains_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N-
> term.png width 2000 height 1448 supersample 4 transparentBackground true
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N-
> term.cxs
——— End of log from Mon Feb 10 10:48:48 2025 ———
opened ChimeraX session
> altlocs show
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N-
> term.cxs
——— End of log from Mon Feb 10 11:08:48 2025 ———
opened ChimeraX session
> addcharge H
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue D6M (net charge -2) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.8/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\fbumb\AppData\Local\Temp\tmpyn773k2q\ante.in.mol2 -fi mol2 -o
C:\Users\fbumb\AppData\Local\Temp\tmpyn773k2q\ante.out.mol2 -fo mol2 -c bcc
-nc -2 -j 5 -s 2 -dr n
(D6M) ``
(D6M) `Welcome to antechamber 20.0: molecular input file processor.`
(D6M) ``
(D6M) `Info: Finished reading file
(C:\Users\fbumb\AppData\Local\Temp\tmpyn773k2q\ante.in.mol2); atoms read (63),
bonds read (62).`
(D6M) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(D6M) `bash.exe: warning: could not find /tmp, please create!`
(D6M) ``
(D6M) ``
(D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(D6M) `bash.exe: warning: could not find /tmp, please create!`
(D6M) `Info: Total number of electrons: 204; net charge: -2`
(D6M) ``
(D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`
(D6M) `bash.exe: warning: could not find /tmp, please create!`
(D6M) ``
(D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.8/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(D6M) `bash.exe: warning: could not find /tmp, please create!`
(D6M) ``
(D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(D6M) `bash.exe: warning: could not find /tmp, please create!`
(D6M) ``
Charges for residue D6M determined
> show H
> show #!2 models
> hide #!2 models
> select #!1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 interModel false intraRes false reveal true log
> true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
35 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 ND1 no hydrogen 3.227 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 O no hydrogen 3.552 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 2.909 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 2.831 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 2.840 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 3.173 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 9 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 3.144 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 10 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 6 O no hydrogen 2.714 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 O no hydrogen 2.777 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 O no hydrogen 2.810 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 O no hydrogen 2.676 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 12 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 O no hydrogen 2.672 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 13 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 9 O no hydrogen 2.527 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 10 O no hydrogen 2.743 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 O no hydrogen 2.520 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 O no hydrogen 3.285 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 18 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 O no hydrogen 3.131 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 O no hydrogen 3.070 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 22 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 18 O no hydrogen 2.724 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ILE 23 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 19 O no hydrogen 2.885 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 20 O no hydrogen 2.722 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TRP 25 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 O no hydrogen 2.871 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 26 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 22 O no hydrogen 2.630 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 27 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ILE 23 O no hydrogen 2.543 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 O no hydrogen 2.776 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 O no hydrogen 2.946 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TRP 25 O no hydrogen 2.884 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
35 hydrogen bonds found
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!6 models
> hide #!4 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!3 models
> hide #!6 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!8 models
> hide #!7 models
> show #!9 models
> hide #!8 models
> show #!5 models
> hide #!5 models
> show #!8 models
> select #8/P
252 atoms, 256 bonds, 30 residues, 1 model selected
> hide sel cartoons
> hide #!9 models
> hide #!10 models
> show #!10 models
> select #10/P
231 atoms, 238 bonds, 28 residues, 1 model selected
> hide sel cartoons
> hide #!10 models
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> show #!5 models
> hide #!5 models
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!1 models
> select #6/P
262 atoms, 267 bonds, 30 residues, 1 model selected
> hide sel cartoons
> hide #!8 models
> select clear
> show #!2 models
> hide #!1 models
> select #2/P
238 atoms, 238 bonds, 8 pseudobonds, 35 residues, 2 models selected
> hide sel cartoons
> select clear
> show #!1 models
> show #!3 models
> select #3/P
245 atoms, 251 bonds, 29 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> show #!5 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide sel cartoons
> select #!1/P#3/P#4/P#5/P#10/P
1184 atoms, 1216 bonds, 290 pseudobonds, 142 residues, 7 models selected
> hide sel & #!1,3-5 cartoons
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> select #8/P
252 atoms, 256 bonds, 30 residues, 1 model selected
> hide #1.3.1.1-2#!1-7 cartoons
> undo
> select #8/P
252 atoms, 256 bonds, 30 residues, 1 model selected
> hide #1.3.1.1-2#!1-7 cartoons
> undo
> select clear
> select #7/P
294 atoms, 298 bonds, 30 residues, 1 model selected
> hide sel cartoons
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> show #!9 models
> select #9/P
236 atoms, 240 bonds, 29 residues, 1 model selected
> hide sel cartoons
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!10 models
> hide #!9 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!8 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!10 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> show #!9 models
> hide #!10 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!7 models
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!8 models
> show #!8 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!8 models
> hide #!7 models
> show #!9 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> hide #!3 models
> show #!3 models
> show #!9 models
> hide #!9 models
> select /R:306
126 atoms, 135 bonds, 9 residues, 9 models selected
> show sel & #!1-2 atoms
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #11 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> select /R
29418 atoms, 30299 bonds, 69 pseudobonds, 3757 residues, 23 models selected
> show sel & #1.3.1.1-2#!1 cartoons
> select /R:300
72 atoms, 63 bonds, 9 residues, 9 models selected
> show sel & #!1 atoms
> show #!8 models
> show #!9 models
> show #!10 models
> show #!3 models
> show #!2 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!4 models
> select /R:233
80 atoms, 70 bonds, 10 residues, 10 models selected
> show sel & #!1-4,8-9 atoms
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!8 models
> hide #!9 models
> select clear
> select #!1/P
232 atoms, 239 bonds, 27 pseudobonds, 28 residues, 2 models selected
> hbonds sel color #000000 interModel false intraRes false reveal true log
> true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
35 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 ND1 no hydrogen 3.227 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 O no hydrogen 3.552 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 2.909 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 2.831 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 2.840 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 3.173 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 9 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 3.144 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 10 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 6 O no hydrogen 2.714 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 O no hydrogen 2.777 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 O no hydrogen 2.810 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 O no hydrogen 2.676 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 12 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 O no hydrogen 2.672 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 13 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 9 O no hydrogen 2.527 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 10 O no hydrogen 2.743 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 O no hydrogen 2.520 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 O no hydrogen 3.285 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 18 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 O no hydrogen 3.131 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 O no hydrogen 3.070 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 22 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 18 O no hydrogen 2.724 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ILE 23 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 19 O no hydrogen 2.885 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 20 O no hydrogen 2.722 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TRP 25 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 O no hydrogen 2.871 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 26 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 22 O no hydrogen 2.630 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 27 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ILE 23 O no hydrogen 2.543 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 O no hydrogen 2.776 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 O no hydrogen 2.946 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TRP 25 O no hydrogen 2.884 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
35 hydrogen bonds found
> hbonds sel color #000000 interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
8 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
9 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.7 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.7 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
11 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A
11 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 21.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 21 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 22.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 22 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 23.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 23 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 24.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 24 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 25.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 25 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 28.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 28 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 30.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 30 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 40.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 40 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
10 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 0.9 angleSlop 40.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.9 angstroms and 40 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A
13 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 1.1 angleSlop 40.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1.1 angstroms and 40 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
21 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 no hydrogen 4.025 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.004 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 OE1 no hydrogen 3.869 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 5 O no hydrogen 3.885 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.025 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 no hydrogen 4.061 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLU 138 OE1 no hydrogen 4.180 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG no hydrogen 4.061 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A
21 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 1.2 angleSlop 40.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1.2 angstroms and 40 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
22 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 no hydrogen 4.025 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.004 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 OE1 no hydrogen 3.869 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 5 O no hydrogen 3.885 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.025 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 no hydrogen 4.061 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLU 138 OE1 no hydrogen 4.180 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG no hydrogen 4.061 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 380 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 4.300 N/A
22 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 1.3 angleSlop 40.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1.3 angstroms and 40 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
25 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 no hydrogen 4.025 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.004 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 OE1 no hydrogen 3.869 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 5 O no hydrogen 3.885 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.025 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 no hydrogen 4.061 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLU 138 OE1 no hydrogen 4.180 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 210 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 OD2 no hydrogen 4.147 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG no hydrogen 4.061 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 299 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 O no hydrogen 4.381 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 ND2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 4.585 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 380 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 4.300 N/A
25 hydrogen bonds found
> hbonds sel color #000000 interModel false distSlop 1.3 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1.3 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
24 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 no hydrogen 4.025 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.004 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 5 O no hydrogen 3.885 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.025 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 no hydrogen 4.061 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLU 138 OE1 no hydrogen 4.180 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 210 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 OD2 no hydrogen 4.147 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG no hydrogen 4.061 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 299 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 O no hydrogen 4.381 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 ND2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 4.585 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 380 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 4.300 N/A
24 hydrogen bonds found
> hbonds sel color #000000 interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 GLP1_BI456906_final_stubbed_checked_20250131.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A
GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A
8 hydrogen bonds found
> show #!2 models
> show #!4 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> select /R:233
80 atoms, 70 bonds, 10 residues, 10 models selected
> select /R:234
90 atoms, 80 bonds, 10 residues, 10 models selected
> select /R:300
72 atoms, 63 bonds, 9 residues, 9 models selected
> show sel atoms
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> hide #!6 models
> hide #!7 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select /R:306
126 atoms, 135 bonds, 9 residues, 9 models selected
> show sel & #!1,10 atoms
> show #!2 models
> hide #!1 models
> close #11
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!10 models
> show #!2 models
> show #!10 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> select /R:202
90 atoms, 80 bonds, 10 residues, 10 models selected
> show sel & #!1-2,10 atoms
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!8 models
> hide #!9 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> hide #!3 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20250212_GLP-!R_all_sidechain_analysis.cxs
——— End of log from Wed Feb 12 19:19:19 2025 ———
opened ChimeraX session
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!6 models
> show #!9 models
> open
> C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/GLP1_BI456906_final_stubbed_checked_20250212.pdb
Chain information for GLP1_BI456906_final_stubbed_checked_20250212.pdb #11
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #11
9031 atoms, 9228 bonds, 4 pseudobonds, 1172 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select #11/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 232 atom styles
> color sel byhetero
> hide #!10 models
> hide #!9 models
> hide #!5 models
> hide #!6 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> close #11
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!6 models
> close #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
[deleted to fit within ticket limits]
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> open
> C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/GLP1_BI456906_final_stubbed_checked_20250212.pdb
Chain information for GLP1_BI456906_final_stubbed_checked_20250212.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #1
9031 atoms, 9228 bonds, 4 pseudobonds, 1172 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> show #!2 models
> mmaker #2-10 to #1/R:139-168,175-203,223-256,262-291,303-336,346-368,377-404
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 GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1070.2
RMSD between 208 pruned atom pairs is 0.508 angstroms; (across all 208 pairs:
0.508)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence
alignment score = 962.8
RMSD between 144 pruned atom pairs is 0.528 angstroms; (across all 144 pairs:
0.528)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence
alignment score = 1085.6
RMSD between 208 pruned atom pairs is 0.656 angstroms; (across all 208 pairs:
0.656)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence
alignment score = 1057.6
RMSD between 208 pruned atom pairs is 0.483 angstroms; (across all 208 pairs:
0.483)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1066.6
RMSD between 206 pruned atom pairs is 0.621 angstroms; (across all 208 pairs:
0.651)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1027.6
RMSD between 208 pruned atom pairs is 0.701 angstroms; (across all 208 pairs:
0.701)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1045
RMSD between 207 pruned atom pairs is 0.490 angstroms; (across all 208 pairs:
0.516)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment
score = 1074.4
RMSD between 208 pruned atom pairs is 0.453 angstroms; (across all 208 pairs:
0.453)
Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with
GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score =
1065.8
RMSD between 207 pruned atom pairs is 0.544 angstroms; (across all 208 pairs:
0.564)
> hide #!2 models
> select #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> show sel atoms
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true makePseudobonds false
> reveal true log true
[deleted to fit within ticket limits]
451 hydrogen bonds found
> select clear
> style #!1 stick
Changed 9031 atom styles
> color #1 byhetero
> select add #1/P
232 atoms, 239 bonds, 28 residues, 1 model selected
> hide sel cartoons
> color sel #87ceebff
> select clear
> select add #1/R
2919 atoms, 3007 bonds, 2 pseudobonds, 378 residues, 2 models selected
> color (#!1 & sel) #dda0ddff
> select clear
> color #1 byhetero
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1/R:300
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> mmaker #1/R:362-391
> matchmaker #1/R:362-391
Missing required "to" argument
> select #1/R:362-391
245 atoms, 250 bonds, 30 residues, 1 model selected
> show sel atoms
> select clear
> select #1/R:379
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/R:382@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/R:382@CG2
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 2 time(s)]
> undo
[Repeated 1 time(s)]
> altlocs show
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!5 models
> dssp
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /R:201,202
170 atoms, 160 bonds, 20 residues, 10 models selected
> show sel & #!1-5 atoms
> select /R:201,202,145
290 atoms, 280 bonds, 30 residues, 10 models selected
> show sel & #!1-5 atoms
> select /R:197-208
964 atoms, 982 bonds, 121 residues, 12 models selected
> show sel & #1.3.2.1-2#!1-5 atoms
> select /R:220
120 atoms, 120 bonds, 10 residues, 10 models selected
> show sel & #!1-5 atoms
> ui tool show H-Bonds
> hbonds sel color #000000 interModel false intraMol false intraRes false
> reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R
PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N;
8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 6x18_GLP-1R_GLP-1_Gs.pdb
3 GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb
4 Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb
5 P15_GLP1R_PublicationFINAL_MattB_25012024.pdb
6 7vbh_P20_GLP-1R_GsiN18.pdb
7 8jip_MEDI0382_GLP-1R_Gs.pdb
8 8jir_SAR425899_GLP-1R_Gs.pdb
9 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb
10 GLP-1R_BI6450_20240906_revised.pdb
1 GLP1_BI456906_final_stubbed_checked_20250212.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select /R:136-147
952 atoms, 967 bonds, 108 residues, 10 models selected
> show sel & #!1-5 atoms
> open
> C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/maps/Consensus/J11_010_volume_map.mrc
Opened J11_010_volume_map.mrc as #11, grid size 288,288,288, pixel 0.85, shown
at level 0.0836, step 2, values float32
> transparency (#!1-5 & sel) 50
> select clear
> transparency #1-5,11 50
> volume #11 level 0.1092
> volume #11 level 0.1019
> volume #11 level 0.1111
> volume #11 level 0.1239
> volume #11 level 0.1129
> volume #11 level 0.09092
> volume #11 level 0.1147
> volume #11 level 0.1037
> open
> C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/maps/ReceptorLOCAL/J20_007_volume_map_resampled_J11.mrc
Opened J20_007_volume_map_resampled_J11.mrc as #12, grid size 288,288,288,
pixel 0.85, shown at level 0.0772, step 2, values float32
> transparency #1-5,11-12 50
> volume #12 step 1
> volume #12 level 0.1071
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
[deleted to fit within ticket limits]
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb
self.destroy()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
[deleted to fit within ticket limits]
> contacts sel intraMol false ignoreHiddenModels true makePseudobonds false
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
12 contacts
atom1 atom2 overlap distance
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 OG1 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 CE (alt loc B) 0.219 3.121
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 OG1 B #1.3.2.2/R LYS 197 CE (alt loc B) 0.219 3.121
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CG2 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 CE (alt loc B) 0.092 3.668
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CG2 B #1.3.2.2/R LYS 197 CE (alt loc B) 0.092 3.668
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 OG1 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 NZ (alt loc B) -0.059 2.759
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 OG1 B #1.3.2.2/R LYS 197 NZ (alt loc B) -0.059 2.759
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CB GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 CE (alt loc B) -0.085 3.845
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CB B #1.3.2.2/R LYS 197 CE (alt loc B) -0.085 3.845
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CG2 A #1.3.2.1/R LYS 197 CE (alt loc A) -0.231 3.991
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CB GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 NZ (alt loc B) -0.283 3.803
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CB B #1.3.2.2/R LYS 197 NZ (alt loc B) -0.283 3.803
GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CG2 A #1.3.3.1/R PHE 230 CE1 (alt loc A) -0.303 3.943
12 contacts
> select clear
> ui tool show "Volume Viewer"
> ui tool show "Model Panel"
> show #!2 models
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20250213_GLP-1R_all_sidechain_analysis.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197': Error while saving session data for
'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager
object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error
while saving session data for 'structure altlocs' -> -> '/R LYS 197'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197': Error while saving session data for
'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager
object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error
while saving session data for 'structure altlocs' -> -> '/R LYS 197'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20250213_GLP-1R_all_sidechain_analysis.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197': Error while saving session data for
'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager
object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error
while saving session data for 'structure altlocs' -> -> '/R LYS 197'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197': Error while saving session data for
'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager
object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error
while saving session data for 'structure altlocs' -> -> '/R LYS 197'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> altlocs hide
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20250213_GLP-1R_all_sidechain_analysis.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197': Error while saving session data for
'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager
object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error
while saving session data for 'structure altlocs' -> -> '/R LYS 197'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 365, 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 "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'structure altlocs' ->
<chimerax.std_commands.altlocs._StructureAltlocManager object at
0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197': Error while saving session data for
'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager
object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at
0x000002975AE64490> '/R LYS 197'
ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error
while saving session data for 'structure altlocs' -> -> '/R LYS 197'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 538.92
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_AU.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: LENOVO
Model: 21DECTO1WW
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 34,009,374,720
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12800H
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Fabian,
--Eric