Opened 8 months ago
Closed 8 months ago
#16849 closed defect (duplicate)
'AtomicStructure' object has no attribute '_alt_loc_changes_handler'
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Analysis | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:\Users\fbumb\OneDrive\MIPS\papers\Survodutide\GLP-1R\20250212_GLP-!R_all_sidechain_analysis.cxs > format session Log from Wed Feb 12 19:19:19 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N- > term.cxs Log from Mon Feb 10 11:08:48 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:\Users\fbumb\OneDrive\MIPS\papers\Survodutide\GLP-1R\TM_aligned\sidechains_individual\20250120_GLP-1R_Surv_sidechains_TM4-5_N- > term.cxs format session Log from Mon Feb 10 10:48:48 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N- > term.cxs Log from Wed Jan 29 12:36:00 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_GCG_sidechains_TM4-5_N- > term.cxs Log from Mon Jan 20 12:03:19 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs Log from Mon Nov 18 14:28:29 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs Log from Tue Oct 15 08:56:43 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs Log from Mon Oct 14 14:03:14 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_bottom.cxs Log from Wed Oct 9 12:11:44 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:\Users\fbumb\OneDrive\MIPS\papers\Survodutide\GLP-1R\20241008_GLP-1R_GLP-1_sidechains_TM4-5_bottom.cxs > format session Log from Wed Oct 9 11:31:24 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_Surv_sidechains_TM4-5_bottom.cxs Log from Tue Oct 8 16:46:02 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241007_GLP-1R_all.cxs Log from Mon Oct 7 16:36:45 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs Log from Fri Oct 4 18:32:41 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs Log from Fri Oct 4 15:19:48 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs Log from Fri Oct 4 12:33:42 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/pdb/GLP-1R_BI456906/GLP1_BI456906_20240906_revised.pdb Chain information for GLP1_BI456906_20240906_revised.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > hide atoms > show cartoons > ui tool show "Color Actions" > set bgColor white > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/6x18_GLP-1R_GLP-1_Gs.pdb 6x18_GLP-1R_GLP-1_Gs.pdb title: GLP-1 peptide hormone bound to glucagon-like peptide-1 (GLP-1) receptor [more info...] Chain information for 6x18_GLP-1R_GLP-1_Gs.pdb #2 --- Chain | Description | UniProt A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394 B | transducin β chain 1 | GBB1_HUMAN 2-340 G | G γ-I | GBG2_HUMAN 5-62 N | NANOBODY35 | P | GLP-1 peptide hormone | GLUC_HUMAN 7-36 R | GLP-1R | GLP1R_HUMAN 24-463 > hide atoms > show cartoons > ui tool show Matchmaker > matchmaker #!2 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1901.3 RMSD between 349 pruned atom pairs is 1.013 angstroms; (across all 378 pairs: 1.559) > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/GLP1R_GCG- > PublicationFINAL_MattB_25012024.pdb Chain information for GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb #3 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > hide atoms > show cartoons > matchmaker #!3 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP1R_GCG- PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence alignment score = 1874.9 RMSD between 306 pruned atom pairs is 0.870 angstroms; (across all 378 pairs: 1.999) > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb Chain information for Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb #4 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > hide atoms > show cartoons > matchmaker #!4 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence alignment score = 1945.1 RMSD between 325 pruned atom pairs is 1.204 angstroms; (across all 378 pairs: 1.694) > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/P15_GLP1R_PublicationFINAL_MattB_25012024.pdb Chain information for P15_GLP1R_PublicationFINAL_MattB_25012024.pdb #5 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > hide atoms > show cartoons > matchmaker #!5 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence alignment score = 1873.4 RMSD between 338 pruned atom pairs is 0.880 angstroms; (across all 371 pairs: 1.535) > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/7vbh_P20_GLP-1R_GsiN18.pdb 7vbh_P20_GLP-1R_GsiN18.pdb title: Cryo-em structure of the gipr/GLP-1R/GCGR triagonist peptide 20-bound human GLP-1R-GS complex [more info...] Chain information for 7vbh_P20_GLP-1R_GsiN18.pdb #6 --- Chain | Description | UniProt A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394 B | transducin β chain 1 | GBB1_RAT 2-340 G | G γ-I | GBG2_BOVIN 2-71 N | nanobody 35 | P | peptide 20 | R | glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463 Non-standard residues in 7vbh_P20_GLP-1R_GsiN18.pdb #6 --- AIB — α-aminoisobutyric acid D6M — N-hexadecanoyl-L-glutamic acid > hide atoms > show cartoons > matchmaker #!6 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1868.3 RMSD between 265 pruned atom pairs is 0.836 angstroms; (across all 378 pairs: 2.278) > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/8jip_MEDI0382_GLP-1R_Gs.pdb 8jip_MEDI0382_GLP-1R_Gs.pdb title: Cryo-em structure of the GLP-1R/GCGR dual agonist MEDI0382-bound human GLP-1R-GS complex [more info...] Chain information for 8jip_MEDI0382_GLP-1R_Gs.pdb #7 --- Chain | Description | UniProt A | guanine nucleotide-binding protein G(S) subunit α isoforms short | B | transducin β chain 1 | GBB1_RAT 2-340 G | G γ-I | GBG2_BOVIN 2-71 N | nanobody 35 | P | MEDI0382 | R | glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463 Non-standard residues in 8jip_MEDI0382_GLP-1R_Gs.pdb #7 --- D6M — N-hexadecanoyl-L-glutamic acid > hide atoms > show cartoons > matchmaker #!7 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1842.5 RMSD between 307 pruned atom pairs is 0.972 angstroms; (across all 376 pairs: 1.711) > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/8jir_SAR425899_GLP-1R_Gs.pdb 8jir_SAR425899_GLP-1R_Gs.pdb title: Cryo-em structure of the GLP-1R/GCGR dual agonist SAR425899-bound human GLP-1R-GS complex [more info...] Chain information for 8jir_SAR425899_GLP-1R_Gs.pdb #8 --- Chain | Description | UniProt A | guanine nucleotide-binding protein G(S) subunit α isoforms short | B | transducin β chain 1 | GBB1_RAT 2-340 G | G γ-I | GBG2_BOVIN 2-71 N | nanobody 35 | P | SAR425899 | R | glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463 Non-standard residues in 8jir_SAR425899_GLP-1R_Gs.pdb #8 --- D6M — N-hexadecanoyl-L-glutamic acid > hide atoms > show cartoons > matchmaker #!8 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1839.5 RMSD between 292 pruned atom pairs is 0.888 angstroms; (across all 376 pairs: 2.073) > dssp > cartoon style helix width 1.0 thickness 0.2 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > ui tool show Matchmaker > select #1/R 2919 atoms, 3011 bonds, 2 pseudobonds, 378 residues, 2 models selected > color (#!1 & sel) forest green > select #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > color sel hot pink > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > dssp > show #!2 models > select #1/R 2919 atoms, 3011 bonds, 2 pseudobonds, 378 residues, 2 models selected > color (#!1 & sel) hot pink > select #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > select #1/R 2919 atoms, 3011 bonds, 2 pseudobonds, 378 residues, 2 models selected > ui tool show "Color Actions" > set bgColor #ffaaffff > set bgColor #ffffffff No target buttons for the coloring action are checked [Repeated 30 time(s)] > color sel plum target c > color sel plum target ac > select #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > color sel deep sky blue target ac > color sel cyan target ac > color sel cornflower blue target ac > color sel powder blue target ac > color sel light sky blue target ac > color sel sky blue target ac > color sel light sky blue target ac > color sel sky blue target ac > select #2/R 3158 atoms, 3239 bonds, 2 pseudobonds, 404 residues, 2 models selected > color sel medium sea green target ac > color sel forest green target ac > color sel dark sea green target ac > color sel medium sea green target ac > select #2/P 238 atoms, 238 bonds, 35 residues, 1 model selected > color sel tomato target ac > color sel coral target ac > color sel light coral target ac > select clear > show #!3 models > select #3/R 5476 atoms, 5555 bonds, 2 pseudobonds, 381 residues, 2 models selected > color sel steel blue target ac > select #3/P 470 atoms, 476 bonds, 29 residues, 1 model selected > color sel rosy brown target ac > color sel khaki target ac > select clear > show #!4 models > hide #!4 models > show #!4 models > select #4/R 3129 atoms, 3231 bonds, 2 pseudobonds, 384 residues, 2 models selected > color sel goldenrod target ac > color sel dark green target ac > color sel goldenrod target ac > select #4/P 245 atoms, 251 bonds, 29 residues, 1 model selected > color sel silver target ac > color sel dark gray target ac > select clear > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > select #5/R 3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected > color sel olive drab target ac [Repeated 1 time(s)] > color sel brown target ac [Repeated 1 time(s)] > color sel olive target ac [Repeated 1 time(s)] > color sel sea green target ac [Repeated 1 time(s)] > color sel medium blue target ac > color sel royal blue target ac > color sel dodger blue target ac [Repeated 1 time(s)] > color sel blue target ac > select #5/P 231 atoms, 237 bonds, 28 residues, 1 model selected > color sel pale green target ac > color sel turquoise target ac > color sel medium aquamarine target ac > color sel chartreuse target ac > color sel lime green target ac > color sel light green target ac > select clear > show #!6 models > hide #!6 models > show #!6 models > select #6/R 3105 atoms, 3204 bonds, 2 pseudobonds, 382 residues, 2 models selected > color sel blue violet target ac > color sel rebecca purple target ac > color sel blue violet target ac > color sel dark orchid target ac > color sel dark magenta target ac > color sel purple target ac [Repeated 1 time(s)] > color sel dark magenta target ac > color sel purple target ac > color sel dark magenta target ac > color sel purple target ac > select #6/P 262 atoms, 267 bonds, 30 residues, 1 model selected > color sel dark olive green target ac > color sel olive drab target ac > select clear > show #!7 models > select #7/R 3109 atoms, 3207 bonds, 1 pseudobond, 386 residues, 2 models selected > color sel maroon target ac > select #7/P 294 atoms, 298 bonds, 30 residues, 1 model selected > color sel cadet blue target ac > color sel thistle target ac [Repeated 1 time(s)] > color sel light steel blue target ac [Repeated 1 time(s)] > color sel medium spring green target ac > color sel lime target ac > color sel yellow green target ac > select clear > show #!8 models > hide #!8 models > show #!8 models > select #8/R 2886 atoms, 2964 bonds, 1 pseudobond, 383 residues, 2 models selected > color sel coral target ac > color sel orange target ac > color sel dark orange target ac > color sel green yellow target ac > color sel lime target ac > color sel light coral target ac > color sel orange red target ac > select #8/P 252 atoms, 256 bonds, 30 residues, 1 model selected > color sel medium purple target ac > select clear > hide #!8 models > hide #!7 models > hide #!6 models > hide #!3 models > hide #!5 models > hide #!4 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > select #8/P 252 atoms, 256 bonds, 30 residues, 1 model selected > color sel dark orchid target ac > select clear > show #!6 models > hide #!8 models > select #6/R 3105 atoms, 3204 bonds, 2 pseudobonds, 382 residues, 2 models selected > color sel rebecca purple target ac > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs > log metadata #3 No models had metadata > log chains #3 Chain information for GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb #3 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > log metadata #3 No models had metadata > log chains #3 Chain information for GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb #3 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > log metadata #3 No models had metadata > log chains #3 Chain information for GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb #3 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > view #3 clip false No displayed objects specified. > color #3 #b42b8bff > undo > show #!3 models > hide #!3 models > show #!3 models > show #!2 models > show #!5 models > show #!4 models > show #!7 models > show #!8 models > show #!4 target m [Repeated 1 time(s)] > view #4 clip false [Repeated 1 time(s)] > show #!4 target m > view #4 clip false > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs > ui tool show "Color Actions" > select #1/R 2919 atoms, 3011 bonds, 2 pseudobonds, 378 residues, 2 models selected > select #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > ui tool show "Color Actions" > select add #1 9028 atoms, 9234 bonds, 4 pseudobonds, 1169 residues, 2 models selected > select subtract #1.1 9028 atoms, 9234 bonds, 1169 residues, 1 model selected > select add #1 9028 atoms, 9234 bonds, 4 pseudobonds, 1169 residues, 2 models selected > select subtract #1 Nothing selected > hide #1.1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > select #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > log metadata #6 Metadata for 7vbh_P20_GLP-1R_GsiN18.pdb #6 --- Title | Cryo-em structure of the gipr/GLP-1R/GCGR triagonist peptide 20-bound human GLP-1R-GS complex Citation | Structural insights INTO multiplexed pharmacological actionsof tirzepatide and peptide 20 At the gip, GLP-1 or glucagonreceptors. PMID: 35217653 Non-standard residues | AIB — α-aminoisobutyric acid D6M — N-hexadecanoyl-L-glutamic acid Gene sources | Homo sapiens (human) Homo sapiens (human) Homo sapiens (human) Homo sapiens (human) Homo sapiens (human) Experimental method | Electron microscopy Resolution | 3.00Å > log chains #6 Chain information for 7vbh_P20_GLP-1R_GsiN18.pdb #6 --- Chain | Description | UniProt A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394 B | transducin β chain 1 | GBB1_RAT 2-340 G | G γ-I | GBG2_BOVIN 2-71 N | nanobody 35 | P | peptide 20 | R | glucagon-like peptide 1 receptor | GLP1R_HUMAN 24-463 > ui tool show "Color Actions" > show #!1 target m [Repeated 1 time(s)] > view #1 clip false [Repeated 1 time(s)] > log metadata #1 No models had metadata > log chains #1 Chain information for GLP1_BI456906_20240906_revised.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > ui tool show "Selection Inspector" > show #1.1 models > hide #!1 models > hide #1.1 models > show #!2 models > ui tool show "Selection Inspector" > select #2/R 3158 atoms, 3239 bonds, 2 pseudobonds, 404 residues, 2 models selected > ui tool show "Selection Inspector" > select #2/P 238 atoms, 238 bonds, 35 residues, 1 model selected > hide #!2 models > show #!3 models > select #3/R 5476 atoms, 5555 bonds, 2 pseudobonds, 381 residues, 2 models selected > select #3/P 470 atoms, 476 bonds, 29 residues, 1 model selected > show #!4 models > hide #!3 models > select #4/R 3129 atoms, 3231 bonds, 2 pseudobonds, 384 residues, 2 models selected > select #4/P 245 atoms, 251 bonds, 29 residues, 1 model selected > hide #!4 models > show #!5 models > select #5/R 3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected > color sel #0055ff atoms > ui tool show "Color Actions" > color sel medium blue target ac > color sel royal blue target ac > color sel navy target ac > color sel medium blue target ac > color sel blue target ac > color sel royal blue target ac > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > hide #!3 models > color (#!5 & sel) #5500ffff > color (#!5 & sel) #00aaffff > color (#!5 & sel) #11d3ffff > color (#!5 & sel) #11cbffff > color (#!5 & sel) #13c8ffff > color (#!5 & sel) #18baffff > color (#!5 & sel) #19baffff > color (#!5 & sel) #1abaffff > color (#!5 & sel) #1cbbffff > color (#!5 & sel) #1dbbffff > color (#!5 & sel) #22bdffff > color (#!5 & sel) #26beffff > color (#!5 & sel) #2abfffff > color (#!5 & sel) #2bbcffff > color (#!5 & sel) #31beffff > color (#!5 & sel) #35bfffff > color (#!5 & sel) #38b9ffff > color (#!5 & sel) #3ab3ffff > color (#!5 & sel) #3cb4ffff > color (#!5 & sel) #3eb2ffff > color (#!5 & sel) #43aeffff > color (#!5 & sel) #47a6ffff > color (#!5 & sel) #47a0ffff > color (#!5 & sel) #479affff > color (#!5 & sel) #4791ffff > color (#!5 & sel) #4687ffff > color (#!5 & sel) #457dffff > color (#!5 & sel) #4164ffff > color (#!5 & sel) #3e58ffff > color (#!5 & sel) #3e51ffff > color (#!5 & sel) #3e4bffff > color (#!5 & sel) #3e51ffff > color (#!5 & sel) #3e61ffff > color (#!5 & sel) #3e71ffff > color (#!5 & sel) #407cffff > color (#!5 & sel) #418affff > color (#!5 & sel) #4394ffff > color (#!5 & sel) #43a7ffff > color (#!5 & sel) #43bdffff > color (#!5 & sel) #43c7ffff > color (#!5 & sel) #43cdffff > color (#!5 & sel) #43d3ffff > color (#!5 & sel) #46d7ffff > color (#!5 & sel) #49e1ffff > color (#!5 & sel) #49e7ffff > color (#!5 & sel) #49e1ffff > color (#!5 & sel) #47ddffff > color (#!5 & sel) #46ddffff > color (#!5 & sel) #41ecffff > color (#!5 & sel) #35ebffff > color (#!5 & sel) #30eaffff > color (#!5 & sel) #2eeaffff > color (#!5 & sel) #2aeaffff > color (#!5 & sel) #2beaffff > color (#!5 & sel) #43d6ffff > color (#!5 & sel) #5cc6ffff > color (#!5 & sel) #63c3ffff > color (#!5 & sel) #67c5ffff > color (#!5 & sel) #6ac6ffff > color (#!5 & sel) #6cc7ffff > color (#!5 & sel) #75caffff > color (#!5 & sel) #7ccbffff > color (#!5 & sel) #7dcbffff > color (#!5 & sel) #7dc7ffff > color (#!5 & sel) #77b2ffff > color (#!5 & sel) #74acffff > color (#!5 & sel) #74a5ffff > color (#!5 & sel) #74a0ffff > color (#!5 & sel) #749effff > color (#!5 & sel) #7499ffff > color (#!5 & sel) #7494ffff > color (#!5 & sel) #7394ffff > color (#!5 & sel) #7091ffff > color (#!5 & sel) #6f95ffff > color (#!5 & sel) #7091ffff > color (#!5 & sel) #7494ffff > color (#!5 & sel) #7595ffff > color (#!5 & sel) #7998ffff > color (#!5 & sel) #7b9affff > color (#!5 & sel) #7d99ffff > color (#!5 & sel) #809cffff > color (#!5 & sel) #819cffff > color (#!5 & sel) #87a1ffff > color (#!5 & sel) #89a3ffff > color (#!5 & sel) #8ba4ffff > color (#!5 & sel) #8baaffff > color (#!5 & sel) #8baeffff > color (#!5 & sel) #8aafffff > color (#!5 & sel) #8ab3ffff > color (#!5 & sel) #89b2ffff > color (#!5 & sel) #89b6ffff > color (#!5 & sel) #89b8ffff > color (#!5 & sel) #89bcffff > color (#!5 & sel) #89beffff > color (#!5 & sel) #89c2ffff > color (#!5 & sel) #89c6ffff > color (#!5 & sel) #87cbffff > color (#!5 & sel) #87d1ffff > color (#!5 & sel) #87dbffff > color (#!5 & sel) #89e5ffff > color (#!5 & sel) #8aefffff > color (#!5 & sel) #8bffffff > color (#!5 & sel) #8efff2ff > color (#!5 & sel) #8effecff > color (#!5 & sel) #8effe7ff > color (#!5 & sel) #8effe8ff > color (#!5 & sel) #8efff6ff > color (#!5 & sel) #8efdffff > color (#!5 & sel) #8fe5ffff > color (#!5 & sel) #8fb2ffff > color (#!5 & sel) #9f92ffff > color (#!5 & sel) #c194ffff > color (#!5 & sel) #cd94ffff > color (#!5 & sel) #d294ffff > color (#!5 & sel) #db94ffff > color (#!5 & sel) #df94ffff > color (#!5 & sel) #ed92ffff > color (#!5 & sel) #e38fffff > color (#!5 & sel) #b686ffff > color (#!5 & sel) #75ffacff > color (#!5 & sel) #74ffacff > color (#!5 & sel) #6cffb6ff > color (#!5 & sel) #69ffd5ff > color (#!5 & sel) #66c4ffff > color (#!5 & sel) #67a9ffff > color (#!5 & sel) #6a8dffff > color (#!5 & sel) #6a8affff > color (#!5 & sel) #6b86ffff > color (#!5 & sel) #6b81ffff > color (#!5 & sel) #6b75ffff > color (#!5 & sel) #856fffff > color (#!5 & sel) #9572ffff > color (#!5 & sel) #9470ffff > color (#!5 & sel) #9970ffff > color (#!5 & sel) #9d70ffff > color (#!5 & sel) #a970ffff > color (#!5 & sel) #aa72ffff > color (#!5 & sel) #af79ffff > color (#!5 & sel) #b17dffff > color (#!5 & sel) #ac7cffff > color (#!5 & sel) #8069ffff > color (#!5 & sel) #6b60ffff > color (#!5 & sel) #695effff > color (#!5 & sel) #6661ffff > color (#!5 & sel) #6a65ffff > color (#!5 & sel) #7c77ffff > color (#!5 & sel) #8b80ffff > color (#!5 & sel) #9d90ffff > color (#!5 & sel) #af9bffff > color (#!5 & sel) #b69effff > color (#!5 & sel) #c1a2ffff > color (#!5 & sel) #c4a2ffff > color (#!5 & sel) #cca7ffff > color (#!5 & sel) #cda9ffff > color (#!5 & sel) #d0a9ffff > color (#!5 & sel) #d4aeffff > color (#!5 & sel) #d4afffff > color (#!5 & sel) #d5b0ffff > color (#!5 & sel) #d6b2ffff > color (#!5 & sel) #dab4ffff > color (#!5 & sel) #dab5ffff > color (#!5 & sel) #dcb5ffff > color (#!5 & sel) #ddb7ffff > color (#!5 & sel) #deb9ffff > color (#!5 & sel) #e1bcffff > color (#!5 & sel) #e5c0ffff > color (#!5 & sel) #eec7ffff > color (#!5 & sel) #edc2ffff > color (#!5 & sel) #e39cffff > color (#!5 & sel) #d677ffff > color (#!5 & sel) #c560ffff > color (#!5 & sel) #c35cffff > color (#!5 & sel) #c155ffff > color (#!5 & sel) #c053ffff > color (#!5 & sel) #b949ffff > color (#!5 & sel) #952bffff > color (#!5 & sel) #851affff > color (#!5 & sel) #7e14ffff > color (#!5 & sel) #5c11ffff > color (#!5 & sel) #4911ffff > color (#!5 & sel) #4111ffff > color (#!5 & sel) #1323ffff > color (#!5 & sel) #1332ffff > color (#!5 & sel) #1336ffff > color (#!5 & sel) #1371ffff > color (#!5 & sel) #138dffff > color (#!5 & sel) #1391ffff > color (#!5 & sel) #1399ffff > color (#!5 & sel) #13a1ffff > color (#!5 & sel) #00aaffff > show #!1 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > color #5 #00699eff > color #5 #00aaffff > color #5 #aaaa7fff > undo > select #5/P 231 atoms, 237 bonds, 28 residues, 1 model selected > ui tool show "Color Actions" > color sel lawn green target ac > color sel green yellow target ac > color sel light green target ac > select #5/R 3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected > color sel burly wood target ac > color sel rosy brown target ac > color sel light steel blue target ac > select #5/P 231 atoms, 237 bonds, 28 residues, 1 model selected > color sel olive drab target ac > select clear > select #5/R 3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected > color sel steel blue target ac > color sel deep sky blue target ac > color sel royal blue target ac > select clear > hide #!5 models > show #!3 models > show #!5 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!5 models > show #!4 models > show #!3 models > show #!5 models > hide #!5 models > show #!5 models > hide #!4 models > hide #!1 models > select #3/R 5476 atoms, 5555 bonds, 2 pseudobonds, 381 residues, 2 models selected > color sel dark cyan target ac > color sel cadet blue target ac > color sel medium turquoise target ac > color sel light sea green target ac > color sel medium sea green target ac > color sel dark olive green target ac > color sel dark sea green target ac > color sel sea green target ac > color sel teal target ac > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!5 models > select clear > show #!2 models > select #2/R 3158 atoms, 3239 bonds, 2 pseudobonds, 404 residues, 2 models selected > color sel forest green target ac > color sel lime green target ac > color sel pale green target ac > color sel light green target ac > color sel aquamarine target ac > color sel medium spring green target ac > select clear > hide #!3 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > show #!3 models > show #!4 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > select #2/R 3158 atoms, 3239 bonds, 2 pseudobonds, 404 residues, 2 models selected > select #2/P 238 atoms, 238 bonds, 35 residues, 1 model selected > select #3/R 5476 atoms, 5555 bonds, 2 pseudobonds, 381 residues, 2 models selected > select #3/P 470 atoms, 476 bonds, 29 residues, 1 model selected > select #4/R 3129 atoms, 3231 bonds, 2 pseudobonds, 384 residues, 2 models selected > select #4/P 245 atoms, 251 bonds, 29 residues, 1 model selected > show #!5 models > select #5/R 3048 atoms, 3146 bonds, 3 pseudobonds, 374 residues, 2 models selected > select #5/P 231 atoms, 237 bonds, 28 residues, 1 model selected > hide #!5 models > show #!6 models > select #6/R 3105 atoms, 3204 bonds, 2 pseudobonds, 382 residues, 2 models selected > select #6/P 262 atoms, 267 bonds, 30 residues, 1 model selected > hide #!6 models > show #!7 models > select #7/R 3109 atoms, 3207 bonds, 1 pseudobond, 386 residues, 2 models selected > select #7/P 294 atoms, 298 bonds, 30 residues, 1 model selected > hide #!7 models > show #!8 models > show #!7 models > hide #!7 models > select #8/R 2886 atoms, 2964 bonds, 1 pseudobond, 383 residues, 2 models selected > select #8/P 252 atoms, 256 bonds, 30 residues, 1 model selected > select clear > hide #!8 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs ——— End of log from Fri Oct 4 12:33:42 2024 ——— opened ChimeraX session > cartoon style helix width 1.5 thickness 0.5 > show #!8 models > hide #!1 models > lighting simple [Repeated 1 time(s)] > graphics silhouettes true > lighting shadows true > lighting shadows false > lighting flat [Repeated 1 time(s)] > lighting simple > select #8/R 2886 atoms, 2964 bonds, 1 pseudobond, 383 residues, 2 models selected > color (#!8 & sel) #ff8c00ff > select clear > hide #!8 models > show #!7 models > show #!6 models > hide #!7 models > hide #!6 models > show #!5 models > select #5/P 231 atoms, 237 bonds, 28 residues, 1 model selected > color sel #aa5500ff > select clear > show #!4 models > hide #!5 models > hide #!4 models > show #!3 models > show #!1 models > hide #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs > select add #1/A#3/A#4/A#5/A 7643 atoms, 7785 bonds, 9 pseudobonds, 929 residues, 8 models selected > select add #1/B#3/B#4/B#5/B 18046 atoms, 18376 bonds, 9 pseudobonds, 2283 residues, 8 models selected > select add #1/G#3/G#4/G#5/G 19764 atoms, 20118 bonds, 9 pseudobonds, 2510 residues, 8 models selected > select add #1/G#3/G#4/G#5/G 19764 atoms, 20118 bonds, 9 pseudobonds, 2510 residues, 8 models selected > select add #2/G#6/G#7/G#8/G 21502 atoms, 21880 bonds, 9 pseudobonds, 2737 residues, 12 models selected > select add #1/N#3/N#4/N#5/N 25367 atoms, 25833 bonds, 9 pseudobonds, 3245 residues, 12 models selected > select add #2/N 26333 atoms, 26816 bonds, 9 pseudobonds, 3376 residues, 12 models selected > select add #2/A#6/A 31040 atoms, 31591 bonds, 14 pseudobonds, 3965 residues, 14 models selected > select add #7/A#8/A 34940 atoms, 35567 bonds, 16 pseudobonds, 4439 residues, 16 models selected > select add #6/N#7/N#8/N 37829 atoms, 38521 bonds, 16 pseudobonds, 4819 residues, 16 models selected > select add #2/B#6/B#7/B#8/B 48235 atoms, 49071 bonds, 16 pseudobonds, 6216 residues, 16 models selected > hide sel & #!1 cartoons > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > show #!4 models > show #!6 models > show #!5 models > show #!7 models > show #!8 models > hide sel cartoons > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_GLP-1_helix_overview.png > width 2000 height 1448 supersample 4 transparentBackground true > hide #!2 models > show #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_GCG_helix_overview.png > width 2000 height 1448 supersample 4 transparentBackground true > hide #!3 models > show #!4 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_Oxyn_helix_overview.png > width 2000 height 1448 supersample 4 transparentBackground true > hide #!4 models > show #!5 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_P15_helix_overview.png > width 2000 height 1448 supersample 4 transparentBackground true > hide #!5 models > show #!6 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_P20_helix_overview.png > width 2000 height 1448 supersample 4 transparentBackground true > hide #!6 models > show #!7 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_MEDI_helix_overview.png > width 2000 height 1448 supersample 4 transparentBackground true > show #!8 models > hide #!7 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_Surv_SAR_helix_overview.png > width 2000 height 1448 supersample 4 transparentBackground true > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs ——— End of log from Fri Oct 4 15:19:48 2024 ——— opened ChimeraX session > hide #!8 models > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/structures_to_compare/7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb title: EX4-D-ala bound to the glucagon-like peptide-1 receptor/G protein complex (conformer 1) [more info...] Chain information for 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb #9 --- Chain | Description | UniProt A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394 B | transducin β chain 1 | GBB1_HUMAN 2-340 G | G γ-I | GBG2_HUMAN 5-62 N | NB35 | P | EX4-D-ala | R | GLP-1R | GLP1R_HUMAN 24-463 Non-standard residues in 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb #9 --- DAL — D-alanine > select clear > hide #!1,9 atoms > select add #9 9160 atoms, 9368 bonds, 4 pseudobonds, 1169 residues, 2 models selected > show sel cartoons > select clear > ui tool show Matchmaker > matchmaker #!9 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment score = 1869.5 RMSD between 291 pruned atom pairs is 0.846 angstroms; (across all 375 pairs: 1.874) > select add #9/G 444 atoms, 450 bonds, 58 residues, 1 model selected > select add #9/N 1417 atoms, 1445 bonds, 186 residues, 1 model selected > select add #9/A 3346 atoms, 3410 bonds, 2 pseudobonds, 419 residues, 2 models selected > select add #9/B 5961 atoms, 6072 bonds, 2 pseudobonds, 759 residues, 2 models selected > hide sel cartoons > select clear > select add #9/P 236 atoms, 240 bonds, 29 residues, 1 model selected > color sel #ff0000ff > select clear > select add #9/R 2963 atoms, 3056 bonds, 2 pseudobonds, 381 residues, 2 models selected > color (#!9 & sel) #8fbc8fff > select clear > cartoon style helix width 1.5 thickness 0.5 > dssp > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241004_GLP-1R_all.cxs ——— End of log from Fri Oct 4 18:32:41 2024 ——— opened ChimeraX session > open > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/pdb/GLP-1R_BI6450/GLP-1R_BI6450_20240906_revised.pdb Chain information for GLP-1R_BI6450_20240906_revised.pdb #10 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available > hide #!1,9-10 atoms > hide #!1 models > hide #!9 models > show #!10 cartoons > cartoon style helix width 1.5 thickness 0.5 > dssp > show #!1 models > ui tool show Matchmaker > matchmaker #!10 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score = 1935.5 RMSD between 355 pruned atom pairs is 0.861 angstroms; (across all 378 pairs: 1.141) > select #10/R 2878 atoms, 2969 bonds, 2 pseudobonds, 378 residues, 2 models selected > color (#!10 & sel) #9093c9ff > select #10/P 231 atoms, 238 bonds, 28 residues, 1 model selected > color sel #dd8ba7ff > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!5 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!9 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > select add #10/A 1844 atoms, 1879 bonds, 2 pseudobonds, 234 residues, 2 models selected > select add #10/B 4418 atoms, 4500 bonds, 2 pseudobonds, 573 residues, 2 models selected > select add #10/G 4792 atoms, 4880 bonds, 2 pseudobonds, 630 residues, 2 models selected > select add #10/N 5756 atoms, 5866 bonds, 2 pseudobonds, 758 residues, 2 models selected > hide sel cartoons > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241007_GLP-1R_all.cxs > show #!6 models > show #!5 models > hide #!5 models > hide #!6 models > hide #!1 models > hide #!10 models > show #!10 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241007_GLP-1R_all.cxs ——— End of log from Mon Oct 7 16:36:45 2024 ——— opened ChimeraX session > show #!1 models > hide #!10 models > select /R:262-337 7015 atoms, 7225 bonds, 760 residues, 10 models selected > hide sel & #!1 cartoons > select #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > show sel atoms > hide sel cartoons > style sel stick Changed 232 atom styles > color sel byhetero > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true makePseudobonds false > reveal true log true [deleted to fit within ticket limits] 447 hydrogen bonds found > select /R:299,300,310,306,298 559 atoms, 549 bonds, 50 residues, 10 models selected > hide sel & #!1 atoms > ribbon suppressBackboneDisplay false > select /R:262-337 7015 atoms, 7225 bonds, 760 residues, 10 models selected > hide sel & #!1 cartoons > select up 7238 atoms, 7446 bonds, 786 residues, 10 models selected > select /R:262-337 7015 atoms, 7225 bonds, 760 residues, 10 models selected > select /R:29-32 241 atoms, 231 bonds, 36 residues, 10 models selected > hide sel & #!1 cartoons > select #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > hide sel cartoons > select clear > select /R:32 76 atoms, 66 bonds, 10 residues, 10 models selected > show sel & #!1 cartoons > select clear > ui tool show "Side View" > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_Surv_sidechains_TM4-5_bottom.cxs ——— End of log from Tue Oct 8 16:46:02 2024 ——— opened ChimeraX session > show #!2 models > hide #!1 models > select /R:262-337 7015 atoms, 7225 bonds, 760 residues, 10 models selected > hide sel & #!2 cartoons > show sel & #!2 cartoons > hide sel & #!2 cartoons > show #!1 models > show sel & #!1-2 cartoons > hide sel & #!1-2 cartoons > hide #!1 models > hide sel & #!2 atoms > select clear > hide #!2 atoms > select #2/P 238 atoms, 238 bonds, 8 pseudobonds, 35 residues, 2 models selected > show sel atoms > hide sel cartoons > select add ::name="HOH" 375 atoms, 238 bonds, 116 pseudobonds, 172 residues, 8 models selected > show sel & #!2 atoms > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > style sel & #!2 stick Changed 331 atom styles > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true makePseudobonds false > reveal true log true [deleted to fit within ticket limits] 450 hydrogen bonds found > select clear > style #!10 stick Changed 8867 atom styles > color #10 byhetero > select /R:262-337 7015 atoms, 7225 bonds, 760 residues, 10 models selected > hide sel & #!10 atoms > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_NLS_sidechains_TM4-5_bottom.cxs > show #!1 models > hide #!10 models > hide #!1 models > show #!2 models > select /R:262-337 7015 atoms, 7225 bonds, 760 residues, 10 models selected > hide sel & #!2 atoms > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > hide sel & #!4 atoms > show #!5 models > hide #!4 models > hide sel & #!5 atoms > hide #!5 models > show #!6 models > show #!7 models > hide #!6 models > show #!8 models > hide #!7 models > show #!9 models > hide #!8 models > show #!10 models > hide #!9 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_bottom.cxs > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #!9 models > hide #!10 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!3 models > hide #!9 models > select add H 9249 atoms, 7225 bonds, 1095 residues, 10 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select clear > select add #3/P 245 atoms, 251 bonds, 29 residues, 1 model selected > select add ::name="HOH" 387 atoms, 251 bonds, 110 pseudobonds, 171 residues, 9 models selected > show sel & #!3 atoms > ui tool show H-Bonds > hbonds sel color #000000 interModel false intraMol false intraRes false > reveal true log true [deleted to fit within ticket limits] 449 hydrogen bonds found > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_GCG_sidechains_TM4-5_bottom.cxs > show #!10 models > hide #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_bottom.cxs > select /R:262-337 5716 atoms, 5905 bonds, 684 residues, 9 models selected > hide sel & #!10 atoms > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_bottom.cxs ——— End of log from Wed Oct 9 12:11:44 2024 ——— opened ChimeraX session > hide #!10 models > show #!1 models > show #!2 models > hide #!1 models > hide sel & #!2 atoms > show #!3 models > hide #!2 models > show #!1 models > show #!2 models > hide #!3 models > hide #!2 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_Surv_TM4-5_bottom.png > width 2000 height 1448 supersample 4 transparentBackground true > hide #!1 models > show #!2 models > ui tool show "Side View" > show #!1 models > hide #!2 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_Surv_TM4-5_bottom.png > width 2000 height 1448 supersample 4 transparentBackground true > hide #!1 models > show #!2 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GLP-1_TM4-5_bottom.png > width 2000 height 1448 supersample 4 transparentBackground true > hide #!2 models > show #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_bottom.png > width 2000 height 1448 supersample 4 transparentBackground true > show #!2 models > hide #!3 models > show #!3 models > show #!1 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > show #!3 models > show #!2 models > select /R:190,241 230 atoms, 220 bonds, 20 residues, 10 models selected > show sel & #!1-3 atoms > select clear > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select /R:233,371 160 atoms, 140 bonds, 20 residues, 10 models selected > show #!2 models > show #!3 models > show sel & #!1-3 atoms > select clear > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select /R:230 110 atoms, 110 bonds, 10 residues, 10 models selected > show sel & #!1-3 atoms > select /R:194 70 atoms, 60 bonds, 10 residues, 10 models selected > show sel & #!1-3 atoms > select /R:394 90 atoms, 80 bonds, 10 residues, 10 models selected > show sel & #!1-3 atoms > hide #!3 models > show #!4 models > hide #!4 models > hide #!2 models > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_Surv_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs > hide #!1 models > show #!2 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GLP-1_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > hide #!2 models > show #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > show #!2 models > select /R:364,367 200 atoms, 190 bonds, 20 residues, 10 models selected > show sel & #!2-3 atoms > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > select clear > show #!2 models > select /R:187,367 220 atoms, 220 bonds, 20 residues, 10 models selected > hide sel & #!2-3 atoms > show #!1 models > hide #!1 models > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > select /R:380 110 atoms, 100 bonds, 10 residues, 10 models selected > hide sel & #!2 atoms > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GLP-1_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > hide #!2 models > show #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > show #!1 models > hide #!3 models > select /R:388 80 atoms, 70 bonds, 10 residues, 10 models selected > show sel & #!1 atoms > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_Surv_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs ——— End of log from Mon Oct 14 14:03:14 2024 ——— opened ChimeraX session > select /R:197 90 atoms, 80 bonds, 10 residues, 10 models selected > show sel & #!1 atoms > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241014_GLP-1R_GCG_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs ——— End of log from Tue Oct 15 08:56:43 2024 ——— opened ChimeraX session > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > mmaker #2-10 to #1/R:139-168,175-203,223-256,262-291,303-336,346-368,377-404 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1066.6 RMSD between 208 pruned atom pairs is 0.530 angstroms; (across all 208 pairs: 0.530) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP1R_GCG- PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence alignment score = 962.8 RMSD between 144 pruned atom pairs is 0.525 angstroms; (across all 144 pairs: 0.525) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence alignment score = 1082 RMSD between 208 pruned atom pairs is 0.677 angstroms; (across all 208 pairs: 0.677) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence alignment score = 1054 RMSD between 208 pruned atom pairs is 0.491 angstroms; (across all 208 pairs: 0.491) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1063 RMSD between 206 pruned atom pairs is 0.633 angstroms; (across all 208 pairs: 0.664) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1024 RMSD between 208 pruned atom pairs is 0.721 angstroms; (across all 208 pairs: 0.721) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1041.4 RMSD between 207 pruned atom pairs is 0.511 angstroms; (across all 208 pairs: 0.536) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment score = 1070.8 RMSD between 208 pruned atom pairs is 0.458 angstroms; (across all 208 pairs: 0.458) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score = 1062.2 RMSD between 207 pruned atom pairs is 0.560 angstroms; (across all 208 pairs: 0.580) > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/20241008_GLP-1R_all_sidechains_TM4-5_N- > term.cxs ——— End of log from Mon Nov 18 14:28:29 2024 ——— opened ChimeraX session > mmaker #2-10 to #1/R:139-168,175-203,223-256,262-291,303-336,346-368,377-404 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1066.6 RMSD between 208 pruned atom pairs is 0.530 angstroms; (across all 208 pairs: 0.530) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP1R_GCG- PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence alignment score = 962.8 RMSD between 144 pruned atom pairs is 0.525 angstroms; (across all 144 pairs: 0.525) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence alignment score = 1082 RMSD between 208 pruned atom pairs is 0.677 angstroms; (across all 208 pairs: 0.677) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence alignment score = 1054 RMSD between 208 pruned atom pairs is 0.491 angstroms; (across all 208 pairs: 0.491) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1063 RMSD between 206 pruned atom pairs is 0.633 angstroms; (across all 208 pairs: 0.664) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1024 RMSD between 208 pruned atom pairs is 0.721 angstroms; (across all 208 pairs: 0.721) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1041.4 RMSD between 207 pruned atom pairs is 0.511 angstroms; (across all 208 pairs: 0.536) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment score = 1070.8 RMSD between 208 pruned atom pairs is 0.458 angstroms; (across all 208 pairs: 0.458) Matchmaker GLP1_BI456906_20240906_revised.pdb, chain R (#1) with GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score = 1062.2 RMSD between 207 pruned atom pairs is 0.560 angstroms; (across all 208 pairs: 0.580) > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!1 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_GLP-1_sidechains_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_GLP-1_sidechains_TM4-5_N- > term.cxs > show #!3 models > hide #!2 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_GCG_sidechains_TM4-5_N- > term.cxs ——— End of log from Mon Jan 20 12:03:19 2025 ——— opened ChimeraX session > show #!1 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > ui tool show H-Bonds > hbonds sel color #434343 radius 0.08 interModel false intraMol false > intraRes false reveal true log true Atom specifier selects no atoms > select /P 2466 atoms, 2515 bonds, 8 pseudobonds, 296 residues, 11 models selected > hbonds sel color #434343 radius 0.08 interModel false intraMol false > intraRes false reveal true log true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N [deleted to fit within ticket limits] 138 hydrogen bonds found > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!3 models > hide #!2 models > hide #!4 models > select clear > hbonds reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N 72154 hydrogen bonds found > hbonds intraModel false intraMol false intraRes false reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N 61828 hydrogen bonds found > hbonds sel intraModel false intraMol false intraRes false reveal true Atom specifier selects no atoms > select /P 2466 atoms, 2515 bonds, 1796 pseudobonds, 296 residues, 11 models selected > hbonds sel intraModel false intraMol false intraRes false reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N 2820 hydrogen bonds found > hbonds sel interModel false intraMol false intraRes false reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N 138 hydrogen bonds found > select add ::name="HOH" 2603 atoms, 2515 bonds, 36 pseudobonds, 433 residues, 12 models selected > hbonds sel color #000000 interModel false intraMol false intraRes false > reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N 544 hydrogen bonds found > select clear > ribbon suppressBackboneDisplay true > select /R:337-425 6695 atoms, 6835 bonds, 8 pseudobonds, 815 residues, 18 models selected > select /R:253-341 6475 atoms, 6676 bonds, 2 pseudobonds, 787 residues, 12 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select clear > select add #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > hide sel cartoons > select clear > select #1/R:240@CG 1 atom, 1 residue, 1 model selected > select #1/R:240 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/R:236 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/R:155 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/R:156 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/R:157 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/R:363@CG 1 atom, 1 residue, 1 model selected > select #1/R:365 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/R:363@CG 1 atom, 1 residue, 1 model selected > select #1/R:363@CG 1 atom, 1 residue, 1 model selected > select #1/R:240 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1/R:236 14 atoms, 12 bonds, 2 residues, 1 model selected > select add #1/R:156 25 atoms, 23 bonds, 3 residues, 1 model selected > select add #1/R:155 31 atoms, 28 bonds, 4 residues, 1 model selected > select add #1/R:239 36 atoms, 32 bonds, 5 residues, 1 model selected > select add #1/R:392 42 atoms, 37 bonds, 2 pseudobonds, 6 residues, 2 models selected > select add #1/R:363@CG 43 atoms, 37 bonds, 2 pseudobonds, 7 residues, 2 models selected > select add #1/R:389 49 atoms, 42 bonds, 2 pseudobonds, 8 residues, 2 models selected > select add #1/R:386 56 atoms, 48 bonds, 2 pseudobonds, 9 residues, 2 models selected > select add #1/R:145 68 atoms, 60 bonds, 2 pseudobonds, 10 residues, 2 models selected > hide sel atoms > select clear > select #1/R:157 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #1/R:239 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/R:240 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/R:185 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/R:186 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #1/R:383 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/R:379 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/R:379 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/R:383 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select /R:363,374 195 atoms, 194 bonds, 20 residues, 10 models selected > hide sel & #!1 atoms > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N- > term.cxs ——— End of log from Wed Jan 29 12:36:00 2025 ——— opened ChimeraX session > close #1 > open > C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/GLP1_BI456906_final_stubbed_checked_20250131.pdb Chain information for GLP1_BI456906_final_stubbed_checked_20250131.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available 9 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!1 atoms > show #!1 cartoons > dssp > cartoon style helix width 1.5 thickness 0.5 > mmaker #2-10 to #1/R:139-168,175-203,223-256,262-291,303-336,346-368,377-404 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with 6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1070.2 RMSD between 208 pruned atom pairs is 0.522 angstroms; (across all 208 pairs: 0.522) Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence alignment score = 962.8 RMSD between 144 pruned atom pairs is 0.528 angstroms; (across all 144 pairs: 0.528) Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence alignment score = 1085.6 RMSD between 208 pruned atom pairs is 0.656 angstroms; (across all 208 pairs: 0.656) Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence alignment score = 1057.6 RMSD between 208 pruned atom pairs is 0.490 angstroms; (across all 208 pairs: 0.490) Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with 7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1066.6 RMSD between 206 pruned atom pairs is 0.633 angstroms; (across all 208 pairs: 0.664) Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with 8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1027.6 RMSD between 208 pruned atom pairs is 0.706 angstroms; (across all 208 pairs: 0.706) Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with 8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1045 RMSD between 206 pruned atom pairs is 0.484 angstroms; (across all 208 pairs: 0.531) Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment score = 1074.4 RMSD between 208 pruned atom pairs is 0.458 angstroms; (across all 208 pairs: 0.458) Matchmaker GLP1_BI456906_final_stubbed_checked_20250131.pdb, chain R (#1) with GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score = 1065.8 RMSD between 207 pruned atom pairs is 0.552 angstroms; (across all 208 pairs: 0.573) > select add #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true makePseudobonds false > reveal true log true [deleted to fit within ticket limits] 449 hydrogen bonds found > select clear > select add #1/R 2919 atoms, 3007 bonds, 2 pseudobonds, 378 residues, 2 models selected > color (#!1 & sel) #dda0ddff > select clear > style #!1 stick Changed 9031 atom styles > color #1,11 byhetero > select /R:253-341 6475 atoms, 6676 bonds, 2 pseudobonds, 787 residues, 12 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select add #1/P 6707 atoms, 6915 bonds, 2 pseudobonds, 815 residues, 12 models selected > hide sel & #!1 cartoons > show sel & #!1 atoms > select clear > select /R:253-341 6475 atoms, 6676 bonds, 2 pseudobonds, 787 residues, 12 models selected > hide sel & #!1 atoms > select /R:190,198,380,388,371 457 atoms, 407 bonds, 50 residues, 10 models selected > show sel & #!1 atoms > select /R:190,198,380,388,371,149 527 atoms, 467 bonds, 60 residues, 10 models selected > show sel & #!1 atoms > select clear > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Ex4_sidechains_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N- > term.png width 2000 height 1448 supersample 4 transparentBackground true > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N- > term.cxs ——— End of log from Mon Feb 10 10:48:48 2025 ——— opened ChimeraX session > altlocs show > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/TM_aligned/sidechains_individual/20250120_GLP-1R_Surv_sidechains_TM4-5_N- > term.cxs ——— End of log from Mon Feb 10 11:08:48 2025 ——— opened ChimeraX session > addcharge H Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue D6M (net charge -2) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.8/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\fbumb\AppData\Local\Temp\tmpyn773k2q\ante.in.mol2 -fi mol2 -o C:\Users\fbumb\AppData\Local\Temp\tmpyn773k2q\ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (D6M) `` (D6M) `Welcome to antechamber 20.0: molecular input file processor.` (D6M) `` (D6M) `Info: Finished reading file (C:\Users\fbumb\AppData\Local\Temp\tmpyn773k2q\ante.in.mol2); atoms read (63), bonds read (62).` (D6M) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (D6M) `bash.exe: warning: could not find /tmp, please create!` (D6M) `` (D6M) `` (D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (D6M) `bash.exe: warning: could not find /tmp, please create!` (D6M) `Info: Total number of electrons: 204; net charge: -2` (D6M) `` (D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out` (D6M) `bash.exe: warning: could not find /tmp, please create!` (D6M) `` (D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX 1.8/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1` (D6M) `bash.exe: warning: could not find /tmp, please create!` (D6M) `` (D6M) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (D6M) `bash.exe: warning: could not find /tmp, please create!` (D6M) `` Charges for residue D6M determined > show H > show #!2 models > hide #!2 models > select #!1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #000000 interModel false intraRes false reveal true log > true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 35 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 ND1 no hydrogen 3.227 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 O no hydrogen 3.552 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 2.909 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 2.831 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 2.840 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 3.173 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 9 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 3.144 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 10 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 6 O no hydrogen 2.714 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 O no hydrogen 2.777 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 O no hydrogen 2.810 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 O no hydrogen 2.676 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 12 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 O no hydrogen 2.672 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 13 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 9 O no hydrogen 2.527 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 10 O no hydrogen 2.743 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 O no hydrogen 2.520 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 O no hydrogen 3.285 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 18 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 O no hydrogen 3.131 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 O no hydrogen 3.070 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 22 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 18 O no hydrogen 2.724 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ILE 23 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 19 O no hydrogen 2.885 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 20 O no hydrogen 2.722 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TRP 25 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 O no hydrogen 2.871 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 26 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 22 O no hydrogen 2.630 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 27 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ILE 23 O no hydrogen 2.543 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 O no hydrogen 2.776 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 O no hydrogen 2.946 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TRP 25 O no hydrogen 2.884 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 35 hydrogen bonds found > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!4 models > hide #!5 models > show #!6 models > hide #!4 models > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!3 models > hide #!6 models > hide #!1 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > show #!5 models > hide #!4 models > hide #!5 models > show #!6 models > show #!7 models > hide #!6 models > show #!8 models > hide #!7 models > show #!9 models > hide #!8 models > show #!5 models > hide #!5 models > show #!8 models > select #8/P 252 atoms, 256 bonds, 30 residues, 1 model selected > hide sel cartoons > hide #!9 models > hide #!10 models > show #!10 models > select #10/P 231 atoms, 238 bonds, 28 residues, 1 model selected > hide sel cartoons > hide #!10 models > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > show #!5 models > hide #!5 models > show #!7 models > show #!6 models > hide #!7 models > show #!1 models > select #6/P 262 atoms, 267 bonds, 30 residues, 1 model selected > hide sel cartoons > hide #!8 models > select clear > show #!2 models > hide #!1 models > select #2/P 238 atoms, 238 bonds, 8 pseudobonds, 35 residues, 2 models selected > hide sel cartoons > select clear > show #!1 models > show #!3 models > select #3/P 245 atoms, 251 bonds, 29 residues, 1 model selected > hide sel cartoons > show #!4 models > show #!5 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide sel cartoons > select #!1/P#3/P#4/P#5/P#10/P 1184 atoms, 1216 bonds, 290 pseudobonds, 142 residues, 7 models selected > hide sel & #!1,3-5 cartoons > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > select #8/P 252 atoms, 256 bonds, 30 residues, 1 model selected > hide #1.3.1.1-2#!1-7 cartoons > undo > select #8/P 252 atoms, 256 bonds, 30 residues, 1 model selected > hide #1.3.1.1-2#!1-7 cartoons > undo > select clear > select #7/P 294 atoms, 298 bonds, 30 residues, 1 model selected > hide sel cartoons > show #!10 models > hide #!10 models > show #!10 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > show #!2 models > show #!9 models > select #9/P 236 atoms, 240 bonds, 29 residues, 1 model selected > hide sel cartoons > select clear > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!5 models > hide #!5 models > show #!3 models > hide #!3 models > hide #!4 models > hide #!10 models > hide #!9 models > hide #11 models > show #11 models > hide #11 models > hide #!8 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!9 models > hide #!9 models > show #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!8 models > hide #!9 models > show #!10 models > show #!3 models > show #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > show #!5 models > show #!6 models > show #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > show #!6 models > show #!9 models > hide #!10 models > hide #!7 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!8 models > hide #!8 models > show #!8 models > show #!7 models > show #!5 models > show #!4 models > hide #!4 models > hide #!3 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > show #!3 models > hide #!3 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!9 models > hide #!9 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!8 models > show #!8 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!3 models > hide #!3 models > hide #!4 models > hide #!8 models > hide #!7 models > show #!9 models > show #!2 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!3 models > hide #!3 models > show #!3 models > hide #!9 models > hide #!3 models > show #!3 models > show #!9 models > hide #!9 models > select /R:306 126 atoms, 135 bonds, 9 residues, 9 models selected > show sel & #!1-2 atoms > show #!4 models > hide #!4 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #11 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > select /R 29418 atoms, 30299 bonds, 69 pseudobonds, 3757 residues, 23 models selected > show sel & #1.3.1.1-2#!1 cartoons > select /R:300 72 atoms, 63 bonds, 9 residues, 9 models selected > show sel & #!1 atoms > show #!8 models > show #!9 models > show #!10 models > show #!3 models > show #!2 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!4 models > select /R:233 80 atoms, 70 bonds, 10 residues, 10 models selected > show sel & #!1-4,8-9 atoms > hide #!2 models > hide #!3 models > hide #!4 models > hide #!8 models > hide #!9 models > select clear > select #!1/P 232 atoms, 239 bonds, 27 pseudobonds, 28 residues, 2 models selected > hbonds sel color #000000 interModel false intraRes false reveal true log > true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 35 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 ND1 no hydrogen 3.227 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 O no hydrogen 3.552 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 2.909 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 2.831 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 2.840 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 3.173 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 9 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 3.144 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 10 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 6 O no hydrogen 2.714 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 O no hydrogen 2.777 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 O no hydrogen 2.810 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 O no hydrogen 2.676 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 12 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 O no hydrogen 2.672 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 13 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 9 O no hydrogen 2.527 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TYR 10 O no hydrogen 2.743 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 O no hydrogen 2.520 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 O no hydrogen 3.285 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 18 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 14 O no hydrogen 3.131 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 O no hydrogen 3.070 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 22 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 18 O no hydrogen 2.724 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ILE 23 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ALA 19 O no hydrogen 2.885 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 20 O no hydrogen 2.722 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TRP 25 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 O no hydrogen 2.871 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LEU 26 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P PHE 22 O no hydrogen 2.630 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 27 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ILE 23 O no hydrogen 2.543 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 O no hydrogen 2.776 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P LYS 24 O no hydrogen 2.946 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 28 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P TRP 25 O no hydrogen 2.884 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 35 hydrogen bonds found > hbonds sel color #000000 interModel false intraMol false intraRes false > reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 8 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 8 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.5 intraMol false > intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 9 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 9 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 intraMol false > intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.7 intraMol false > intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.7 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 11 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A 11 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 intraMol false > intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 21.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 21 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 22.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 22 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 23.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 23 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 24.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 24 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 25.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 25 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 28.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 28 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 30.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 30 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.6 angleSlop 40.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.6 angstroms and 40 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 10 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 10 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 0.9 angleSlop 40.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.9 angstroms and 40 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 13 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A 13 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 1.1 angleSlop 40.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 1.1 angstroms and 40 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 21 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 no hydrogen 4.025 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.004 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 OE1 no hydrogen 3.869 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 5 O no hydrogen 3.885 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.025 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 no hydrogen 4.061 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLU 138 OE1 no hydrogen 4.180 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG no hydrogen 4.061 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A 21 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 1.2 angleSlop 40.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 1.2 angstroms and 40 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 22 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 no hydrogen 4.025 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.004 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 OE1 no hydrogen 3.869 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 5 O no hydrogen 3.885 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.025 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 no hydrogen 4.061 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLU 138 OE1 no hydrogen 4.180 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG no hydrogen 4.061 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 380 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 4.300 N/A 22 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 1.3 angleSlop 40.0 > intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 1.3 angstroms and 40 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 25 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 no hydrogen 4.025 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.004 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 OE1 no hydrogen 3.869 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 5 O no hydrogen 3.885 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.025 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 no hydrogen 4.061 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLU 138 OE1 no hydrogen 4.180 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 210 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 OD2 no hydrogen 4.147 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG no hydrogen 4.061 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 299 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 O no hydrogen 4.381 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 ND2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 4.585 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 380 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 4.300 N/A 25 hydrogen bonds found > hbonds sel color #000000 interModel false distSlop 1.3 intraMol false > intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 1.3 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 24 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 no hydrogen 4.025 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 8 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.842 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.004 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P 192 2 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 5 O no hydrogen 3.885 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 4 O no hydrogen 3.827 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O no hydrogen 4.025 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 O no hydrogen 3.598 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 no hydrogen 4.061 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ARG 17 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLU 138 OE1 no hydrogen 4.180 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 O no hydrogen 3.737 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 210 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 21 OD2 no hydrogen 4.147 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 298 OG1 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 OG no hydrogen 4.061 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 299 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 11 O no hydrogen 4.381 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P SER 8 OG no hydrogen 3.694 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ASN 300 ND2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLY 4 O no hydrogen 4.585 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R ARG 380 NH2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 5 O no hydrogen 4.300 N/A 24 hydrogen bonds found > hbonds sel color #000000 interModel false intraMol false intraRes false > reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 GLP1_BI456906_final_stubbed_checked_20250131.pdb 8 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 7 O GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 O no hydrogen 3.064 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/C HOH 6 O no hydrogen 2.453 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE1 no hydrogen 2.808 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R THR 29 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLU 16 OE2 no hydrogen 3.046 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LEU 32 N GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P ASP 15 OD1 no hydrogen 3.098 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P GLN 3 OE1 no hydrogen 2.815 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R LYS 197 NZ (alt loc B) GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P THR 7 OG1 no hydrogen 2.759 N/A GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/R GLN 234 NE2 GLP1_BI456906_final_stubbed_checked_20250131.pdb #!1/P HIS 1 NE2 no hydrogen 3.164 N/A 8 hydrogen bonds found > show #!2 models > show #!4 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!2 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > select /R:233 80 atoms, 70 bonds, 10 residues, 10 models selected > select /R:234 90 atoms, 80 bonds, 10 residues, 10 models selected > select /R:300 72 atoms, 63 bonds, 9 residues, 9 models selected > show sel atoms > hide #!9 models > show #!9 models > hide #!8 models > hide #!9 models > hide #!6 models > hide #!7 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > select /R:306 126 atoms, 135 bonds, 9 residues, 9 models selected > show sel & #!1,10 atoms > show #!2 models > hide #!1 models > close #11 > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > show #!3 models > show #!5 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!10 models > show #!2 models > show #!10 models > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!4 models > hide #!3 models > select /R:202 90 atoms, 80 bonds, 10 residues, 10 models selected > show sel & #!1-2,10 atoms > show #!3 models > show #!4 models > show #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!8 models > hide #!9 models > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!2 models > hide #!3 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20250212_GLP-!R_all_sidechain_analysis.cxs ——— End of log from Wed Feb 12 19:19:19 2025 ——— opened ChimeraX session > show #!2 models > show #!3 models > show #!4 models > show #!5 models > hide #!4 models > hide #!3 models > show #!6 models > show #!9 models > open > C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/GLP1_BI456906_final_stubbed_checked_20250212.pdb Chain information for GLP1_BI456906_final_stubbed_checked_20250212.pdb #11 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available 18 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select #11 9031 atoms, 9228 bonds, 4 pseudobonds, 1172 residues, 2 models selected > hide sel atoms > show sel cartoons > select clear > select #11/P 232 atoms, 239 bonds, 28 residues, 1 model selected > show sel atoms > style sel stick Changed 232 atom styles > color sel byhetero > hide #!10 models > hide #!9 models > hide #!5 models > hide #!6 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > hide #!9 models > show #!9 models > show #!10 models > hide #!10 models > show #!10 models > close #11 > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!6 models > close #1 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. [deleted to fit within ticket limits] Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > open > C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/GLP1_BI456906_final_stubbed_checked_20250212.pdb Chain information for GLP1_BI456906_final_stubbed_checked_20250212.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available P | No description available R | No description available 18 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select #1 9031 atoms, 9228 bonds, 4 pseudobonds, 1172 residues, 2 models selected > hide sel atoms > show sel cartoons > show #!2 models > mmaker #2-10 to #1/R:139-168,175-203,223-256,262-291,303-336,346-368,377-404 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with 6x18_GLP-1R_GLP-1_Gs.pdb, chain R (#2), sequence alignment score = 1070.2 RMSD between 208 pruned atom pairs is 0.508 angstroms; (across all 208 pairs: 0.508) Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb, chain R (#3), sequence alignment score = 962.8 RMSD between 144 pruned atom pairs is 0.528 angstroms; (across all 144 pairs: 0.528) Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb, chain R (#4), sequence alignment score = 1085.6 RMSD between 208 pruned atom pairs is 0.656 angstroms; (across all 208 pairs: 0.656) Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with P15_GLP1R_PublicationFINAL_MattB_25012024.pdb, chain R (#5), sequence alignment score = 1057.6 RMSD between 208 pruned atom pairs is 0.483 angstroms; (across all 208 pairs: 0.483) Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with 7vbh_P20_GLP-1R_GsiN18.pdb, chain R (#6), sequence alignment score = 1066.6 RMSD between 206 pruned atom pairs is 0.621 angstroms; (across all 208 pairs: 0.651) Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with 8jip_MEDI0382_GLP-1R_Gs.pdb, chain R (#7), sequence alignment score = 1027.6 RMSD between 208 pruned atom pairs is 0.701 angstroms; (across all 208 pairs: 0.701) Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with 8jir_SAR425899_GLP-1R_Gs.pdb, chain R (#8), sequence alignment score = 1045 RMSD between 207 pruned atom pairs is 0.490 angstroms; (across all 208 pairs: 0.516) Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb, chain R (#9), sequence alignment score = 1074.4 RMSD between 208 pruned atom pairs is 0.453 angstroms; (across all 208 pairs: 0.453) Matchmaker GLP1_BI456906_final_stubbed_checked_20250212.pdb, chain R (#1) with GLP-1R_BI6450_20240906_revised.pdb, chain R (#10), sequence alignment score = 1065.8 RMSD between 207 pruned atom pairs is 0.544 angstroms; (across all 208 pairs: 0.564) > hide #!2 models > select #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > show sel atoms > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true makePseudobonds false > reveal true log true [deleted to fit within ticket limits] 451 hydrogen bonds found > select clear > style #!1 stick Changed 9031 atom styles > color #1 byhetero > select add #1/P 232 atoms, 239 bonds, 28 residues, 1 model selected > hide sel cartoons > color sel #87ceebff > select clear > select add #1/R 2919 atoms, 3007 bonds, 2 pseudobonds, 378 residues, 2 models selected > color (#!1 & sel) #dda0ddff > select clear > color #1 byhetero > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select #1/R:300 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > mmaker #1/R:362-391 > matchmaker #1/R:362-391 Missing required "to" argument > select #1/R:362-391 245 atoms, 250 bonds, 30 residues, 1 model selected > show sel atoms > select clear > select #1/R:379 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/R:382@CB 1 atom, 1 residue, 1 model selected > hide sel atoms > select #1/R:382@CG2 1 atom, 1 residue, 1 model selected > hide sel atoms [Repeated 2 time(s)] > undo [Repeated 1 time(s)] > altlocs show > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > show #!5 models > dssp > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select /R:201,202 170 atoms, 160 bonds, 20 residues, 10 models selected > show sel & #!1-5 atoms > select /R:201,202,145 290 atoms, 280 bonds, 30 residues, 10 models selected > show sel & #!1-5 atoms > select /R:197-208 964 atoms, 982 bonds, 121 residues, 12 models selected > show sel & #1.3.2.1-2#!1-5 atoms > select /R:220 120 atoms, 120 bonds, 10 residues, 10 models selected > show sel & #!1-5 atoms > ui tool show H-Bonds > hbonds sel color #000000 interModel false intraMol false intraRes false > reveal true log true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 54 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 73 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 56 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 77 N; 8jir_SAR425899_GLP-1R_Gs.pdb #8/R PRO 55 N Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2 6x18_GLP-1R_GLP-1_Gs.pdb 3 GLP1R_GCG-PublicationFINAL_MattB_25012024.pdb 4 Oxyn_GLP1R_PublicationFinal_Matt_25012024.pdb 5 P15_GLP1R_PublicationFINAL_MattB_25012024.pdb 6 7vbh_P20_GLP-1R_GsiN18.pdb 7 8jip_MEDI0382_GLP-1R_Gs.pdb 8 8jir_SAR425899_GLP-1R_Gs.pdb 9 7s1m_Exendin_4_GLP-1R_DNGs_conformer_1.pdb 10 GLP-1R_BI6450_20240906_revised.pdb 1 GLP1_BI456906_final_stubbed_checked_20250212.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select /R:136-147 952 atoms, 967 bonds, 108 residues, 10 models selected > show sel & #!1-5 atoms > open > C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/maps/Consensus/J11_010_volume_map.mrc Opened J11_010_volume_map.mrc as #11, grid size 288,288,288, pixel 0.85, shown at level 0.0836, step 2, values float32 > transparency (#!1-5 & sel) 50 > select clear > transparency #1-5,11 50 > volume #11 level 0.1092 > volume #11 level 0.1019 > volume #11 level 0.1111 > volume #11 level 0.1239 > volume #11 level 0.1129 > volume #11 level 0.09092 > volume #11 level 0.1147 > volume #11 level 0.1037 > open > C:/Users/fbumb/OneDrive/MIPS/GCGR_GLP1-R/BI_Project/GLP-1R_BI456906_300kV/modelling/maps/ReceptorLOCAL/J20_007_volume_map_resampled_J11.mrc Opened J20_007_volume_map_resampled_J11.mrc as #12, grid size 288,288,288, pixel 0.85, shown at level 0.0772, step 2, values float32 > transparency #1-5,11-12 50 > volume #12 step 1 > volume #12 level 0.1071 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. [deleted to fit within ticket limits] Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 305, in _models_closed_cb self.destroy() File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' Error processing trigger "remove models": AttributeError: 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\std_commands\altlocs.py", line 172, in destroy alt_loc_s._alt_loc_changes_handler.remove() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. [deleted to fit within ticket limits] > contacts sel intraMol false ignoreHiddenModels true makePseudobonds false > reveal true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: False 12 contacts atom1 atom2 overlap distance GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 OG1 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 CE (alt loc B) 0.219 3.121 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 OG1 B #1.3.2.2/R LYS 197 CE (alt loc B) 0.219 3.121 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CG2 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 CE (alt loc B) 0.092 3.668 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CG2 B #1.3.2.2/R LYS 197 CE (alt loc B) 0.092 3.668 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 OG1 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 NZ (alt loc B) -0.059 2.759 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 OG1 B #1.3.2.2/R LYS 197 NZ (alt loc B) -0.059 2.759 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CB GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 CE (alt loc B) -0.085 3.845 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CB B #1.3.2.2/R LYS 197 CE (alt loc B) -0.085 3.845 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CG2 A #1.3.2.1/R LYS 197 CE (alt loc A) -0.231 3.991 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CB GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/R LYS 197 NZ (alt loc B) -0.283 3.803 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CB B #1.3.2.2/R LYS 197 NZ (alt loc B) -0.283 3.803 GLP1_BI456906_final_stubbed_checked_20250213.pdb #!1/P THR 7 CG2 A #1.3.3.1/R PHE 230 CE1 (alt loc A) -0.303 3.943 12 contacts > select clear > ui tool show "Volume Viewer" > ui tool show "Model Panel" > show #!2 models > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20250213_GLP-1R_all_sidechain_analysis.cxs Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 296, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\models.py", line 365, in take_snapshot 'positions': self.positions.array(), ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 273, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 301, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 646, in save mgr.discovery(self._state_containers) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197': Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error while saving session data for 'structure altlocs' -> -> '/R LYS 197' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 296, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\models.py", line 365, in take_snapshot 'positions': self.positions.array(), ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 273, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 301, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 127, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 62, in display run(session, cmd) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 646, in save mgr.discovery(self._state_containers) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197': Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error while saving session data for 'structure altlocs' -> -> '/R LYS 197' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20250213_GLP-1R_all_sidechain_analysis.cxs Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 296, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\models.py", line 365, in take_snapshot 'positions': self.positions.array(), ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 273, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 301, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 646, in save mgr.discovery(self._state_containers) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197': Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error while saving session data for 'structure altlocs' -> -> '/R LYS 197' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 296, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\models.py", line 365, in take_snapshot 'positions': self.positions.array(), ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 273, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 301, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 127, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 62, in display run(session, cmd) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 646, in save mgr.discovery(self._state_containers) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197': Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error while saving session data for 'structure altlocs' -> -> '/R LYS 197' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > altlocs hide > save > C:/Users/fbumb/OneDrive/MIPS/papers/Survodutide/GLP-1R/20250213_GLP-1R_all_sidechain_analysis.cxs Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 296, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\models.py", line 365, in take_snapshot 'positions': self.positions.array(), ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 273, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 301, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 646, in save mgr.discovery(self._state_containers) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197': Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error while saving session data for 'structure altlocs' -> -> '/R LYS 197' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 296, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\models.py", line 365, in take_snapshot 'positions': self.positions.array(), ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 273, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 301, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 127, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 62, in display run(session, cmd) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 646, in save mgr.discovery(self._state_containers) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197': Error while saving session data for 'structure altlocs' -> <chimerax.std_commands.altlocs._StructureAltlocManager object at 0x000002975ADDFB90> -> <chimerax.core.models.Model object at 0x000002975AE64490> '/R LYS 197' ValueError: error processing: 'structure altlocs' -> -> '/R LYS 197': Error while saving session data for 'structure altlocs' -> -> '/R LYS 197' File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 277, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 538.92 OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_AU.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: LENOVO Model: 21DECTO1WW OS: Microsoft Windows 11 Pro (Build 26100) Memory: 34,009,374,720 MaxProcessMemory: 137,438,953,344 CPU: 20 12th Gen Intel(R) Core(TM) i7-12800H OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2024.6.2 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.1 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 WMI: 1.5.1
Change History (2)
comment:1 by , 8 months ago
Component: | Unassigned → Structure Analysis |
---|---|
Description: | modified (diff) |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' |
comment:2 by , 8 months ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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Hi Fabian,
--Eric