Opened 8 months ago

Closed 8 months ago

#16849 closed defect (duplicate)

'AtomicStructure' object has no attribute '_alt_loc_changes_handler'

Reported by: fabian.bumbak@… 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 Eric Pettersen)

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

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> show #!10 models

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> show #!10 models

> hide #!9 models

> hide #!1 models

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> show #!1 models

> hide #!1 models

> show #!1 models

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> show #!1 models

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> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

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> show #!2 models

> hide #!2 models

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> show #!3 models

> hide #!3 models

> show #!3 models

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> show #!4 models

> hide #!4 models

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> 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

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> 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

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> 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
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
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    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 Eric Pettersen, 8 months ago

Component: UnassignedStructure Analysis
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submission'AtomicStructure' object has no attribute '_alt_loc_changes_handler'

comment:2 by Eric Pettersen, 8 months ago

Resolution: duplicate
Status: acceptedclosed

Hi Fabian,

Thanks for reporting this problem. It has been fixed in later releases of ChimeraX, so if you upgrade your version then I think things will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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