id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15372 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.8rc202405171936 (2024-05-17 19:36:10 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2251 in changes File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py"", line 36 in check_for_changes File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 69 in draw_new_frame File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 285 in event_loop File 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All rights reserved. How to cite UCSF ChimeraX > open /Users/maryam/Downloads/6k3f.pdb 6k3f.pdb title: Crystal structure of β-arrestin 2 In complex with CXCR7 phosphopeptide [more info...] Chain information for 6k3f.pdb #1 --- Chain | Description | UniProt A B C D E F | arrestin β-2 | ARRB2_RAT 1-356 U V W X Y Z | peptide from atypical chemokine receptor 3 | ACKR3_HUMAN 331-345 > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 16746 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C /D /E /F Alignment identifier is 1 > select clear > select /A,C-D,F:280-350/B,E:280-346 3198 atoms, 3228 bonds, 418 residues, 1 model selected > select /A,C-D,F:8-350/B,E:8-346 16176 atoms, 16535 bonds, 2 pseudobonds, 2038 residues, 2 models selected > show (#!1 & sel) target ab > hide (#!1 & sel) target a > color (#!1 & sel) yellow > undo > select add #1 17270 atoms, 17104 bonds, 2 pseudobonds, 2629 residues, 2 models selected > select subtract #1 Nothing selected > open /Users/maryam/Downloads/8j9k.pdb 8j9k.pdb title: Structure of basal β-ARRESTIN2 [more info...] Chain information for 8j9k.pdb #2 --- Chain | Description | UniProt B | FAB6 light chain | C | arrestin β-2 | ARRB2_RAT 6-399 D | FAB6 heavy chain | > ui tool show Matchmaker > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6k3f.pdb, chain D (#1) with 8j9k.pdb, chain C (#2), sequence alignment score = 1568.9 RMSD between 194 pruned atom pairs is 1.276 angstroms; (across all 342 pairs: 2.819) > open /Users/maryam/Downloads/8hst.pdb 8hst.pdb title: The structure of rat β-ARRESTIN1 [more info...] Chain information for 8hst.pdb #3 --- Chain | Description | UniProt A B | arrestin β-1 | ARRB1_RAT 1-394 > hide #!1 models > hide #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/U #1/V #1/W #1/X #1/Y #1/Z Alignment identifier is 1 > open /Users/maryam/Downloads/8hsv.pdb 8hsv.pdb title: The structure of rat β-ARRESTIN1 In complex with A rat MDM2 peptide [more info...] Chain information for 8hsv.pdb #4 --- Chain | Description | UniProt A B | arrestin β-1 | ARRB1_RAT 1-394 E F | peptide from E3 ubiquitin-protein ligase MDM2 | D3ZVH5_RAT 210-227 Non-standard residues in 8hsv.pdb #4 --- SO4 — sulfate ion > hide #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #4/E #4/F Alignment identifier is 1 > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A #3/B #4/A #4/B Alignment identifier is 2 > select #3/A-B:394 #4/A-B:394 36 atoms, 32 bonds, 4 residues, 2 models selected > select #3/A-B:4-394 #4/A-B:4-394 11506 atoms, 11742 bonds, 8 pseudobonds, 1448 residues, 4 models selected Arrestin Β-1 [ID: 2] region 4 chains [1-414] RMSD: 47.103 > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) > open > /Users/maryam/Downloads/fold_bai1_vdv_2024_06_02_04_50/fold_bai1_vdv_2024_06_02_04_50_model_0.cif Chain information for fold_bai1_vdv_2024_06_02_04_50_model_0.cif #5 --- Chain | Description A | . > ui tool show Matchmaker > matchmaker #!4 to #5 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 fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with 8hsv.pdb, chain E (#4), sequence alignment score = 28.6 RMSD between 4 pruned atom pairs is 1.633 angstroms; (across all 15 pairs: 8.627) > color #4 #711decff > set bgColor white > color #4 #49278aff > color #4 #47268aff > color #5 #ef6051ff > color #5 #ef725fff > color #5 #ef735fff > color #5 #ef6150ff > color #5 #232eefff > color #5 #ef7c7bff > color #5 #ef6056ff > color #5 #ef7078ff > color #5 #ef6b62ff > color #4 #322896ff > select add #4/A:502@O4 5759 atoms, 5880 bonds, 4 pseudobonds, 723 residues, 3 models selected > select add #4/A:501@S 5760 atoms, 5883 bonds, 4 pseudobonds, 724 residues, 3 models selected > select add #4/A:501@O3 5761 atoms, 5886 bonds, 4 pseudobonds, 724 residues, 3 models selected > select add #4/A:501@O4 5762 atoms, 5886 bonds, 4 pseudobonds, 724 residues, 3 models selected > select add #4/A:502@O1 5763 atoms, 5887 bonds, 4 pseudobonds, 724 residues, 3 models selected > select subtract #4/A:502@O4 5762 atoms, 5887 bonds, 4 pseudobonds, 724 residues, 3 models selected > select add #4/A:503@O3 5763 atoms, 5887 bonds, 4 pseudobonds, 725 residues, 3 models selected > select add #4/A:503@O4 5764 atoms, 5886 bonds, 4 pseudobonds, 725 residues, 3 models selected > select subtract #4/A:503@O4 5763 atoms, 5886 bonds, 4 pseudobonds, 725 residues, 3 models selected > select add #4/B:502@O2 5764 atoms, 5889 bonds, 4 pseudobonds, 726 residues, 3 models selected > select add #4/B:501@O2 5765 atoms, 5891 bonds, 4 pseudobonds, 727 residues, 3 models selected > select add #4/E:219 5771 atoms, 5896 bonds, 4 pseudobonds, 728 residues, 3 models selected > select add #4/E:218 5781 atoms, 5906 bonds, 4 pseudobonds, 729 residues, 3 models selected > select add #4/E:216 5787 atoms, 5911 bonds, 4 pseudobonds, 730 residues, 3 models selected > select add #4/E:215 5794 atoms, 5917 bonds, 4 pseudobonds, 731 residues, 3 models selected > select add #4/E:214 5798 atoms, 5920 bonds, 4 pseudobonds, 732 residues, 3 models selected > select add #4/E:213 5806 atoms, 5927 bonds, 4 pseudobonds, 733 residues, 3 models selected > select add #4/E:211 5814 atoms, 5934 bonds, 4 pseudobonds, 734 residues, 3 models selected > select add #4/E:212 5822 atoms, 5941 bonds, 4 pseudobonds, 735 residues, 3 models selected > select add #4/E:217 5830 atoms, 5948 bonds, 4 pseudobonds, 736 residues, 3 models selected > select add #4/E:220 5835 atoms, 5952 bonds, 4 pseudobonds, 737 residues, 3 models selected > select add #4/E:221 5843 atoms, 5959 bonds, 4 pseudobonds, 738 residues, 3 models selected > select add #4/E:222 5849 atoms, 5964 bonds, 4 pseudobonds, 739 residues, 3 models selected > select add #4/E:223 5857 atoms, 5971 bonds, 4 pseudobonds, 740 residues, 3 models selected > select add #4/E:224 5865 atoms, 5978 bonds, 4 pseudobonds, 741 residues, 3 models selected > select add #4/E:225 5874 atoms, 5986 bonds, 4 pseudobonds, 742 residues, 3 models selected > select add #4/F:225 5883 atoms, 5994 bonds, 4 pseudobonds, 743 residues, 3 models selected > select add #4/F:224 5891 atoms, 6001 bonds, 4 pseudobonds, 744 residues, 3 models selected > select add #4/F:223 5899 atoms, 6008 bonds, 4 pseudobonds, 745 residues, 3 models selected > select add #4/F:221 5907 atoms, 6015 bonds, 4 pseudobonds, 746 residues, 3 models selected > select add #4/F:222 5913 atoms, 6020 bonds, 4 pseudobonds, 747 residues, 3 models selected > select add #4/F:216 5919 atoms, 6025 bonds, 4 pseudobonds, 748 residues, 3 models selected > select add #4/F:214 5923 atoms, 6028 bonds, 4 pseudobonds, 749 residues, 3 models selected > select add #4/F:215 5930 atoms, 6034 bonds, 4 pseudobonds, 750 residues, 3 models selected > select add #4/F:213 5938 atoms, 6041 bonds, 4 pseudobonds, 751 residues, 3 models selected > select add #4/F:212 5946 atoms, 6048 bonds, 4 pseudobonds, 752 residues, 3 models selected > show (#!4 & sel) target ab > hbonds sel & #!4 reveal true 7 hydrogen bonds found > select sel : hbonds sel & #5#!4 reveal true 282 hydrogen bonds found > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A Alignment identifier is 5/A > select #5/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:1-589 4439 atoms, 4559 bonds, 17 pseudobonds, 589 residues, 2 models selected > delete :1-928 > delete :1208-1584 > open /Users/maryam/Downloads/8hsv.pdb 8hsv.pdb title: The structure of rat β-ARRESTIN1 In complex with A rat MDM2 peptide [more info...] Chain information for 8hsv.pdb #1 --- Chain | Description | UniProt A B | arrestin β-1 | ARRB1_RAT 1-394 E F | peptide from E3 ubiquitin-protein ligase MDM2 | D3ZVH5_RAT 210-227 Non-standard residues in 8hsv.pdb #1 --- SO4 — sulfate ion > ui tool show Matchmaker > matchmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8hsv.pdb, chain E (#1) with fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment score = 16.6 RMSD between 4 pruned atom pairs is 1.484 angstroms; (across all 15 pairs: 12.815) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B Alignment identifier is 1 > select #1/A-B:394 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A-B:4-394 5748 atoms, 5866 bonds, 4 pseudobonds, 726 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > ui tool show Matchmaker > matchmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8hsv.pdb, chain E (#1) with fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment score = 16.6 RMSD between 4 pruned atom pairs is 1.484 angstroms; (across all 15 pairs: 12.815) > select #5/A:971 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:971 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > color sel yellow > select #5/A:971 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:971 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > open /Users/maryam/Downloads/1rv1.pdb 1rv1.pdb title: Crystal structure of human MDM2 with an imidazoline inhibitor [more info...] Chain information for 1rv1.pdb #2 --- Chain | Description | UniProt A B C | ubiquitin-protein ligase E3 MDM2 | MDM2_HUMAN 25-109 Non-standard residues in 1rv1.pdb #2 --- IMZ — cis-[4,5-bis-(4-bromophenyl)-2-(2-ethoxy-4-methoxyphenyl)-4,5-dihydroimidazol-1-yl]-[4-(2-hydroxyethyl)piperazin-1-yl]methanone > open /Users/maryam/Downloads/1ycr.pdb 1ycr.pdb title: MDM2 bound to the transactivation domain of P53 [more info...] Chain information for 1ycr.pdb #3 --- Chain | Description | UniProt A | MDM2 | MDM2_HUMAN 17-125 B | P53 | P53_HUMAN 15-29 > open /Users/maryam/Downloads/4hfz.pdb 4hfz.pdb title: Crystal structure of an MDM2/P53 peptide complex [more info...] Chain information for 4hfz.pdb #4 --- Chain | Description | UniProt A C | E3 ubiquitin-protein ligase MDM2 | MDM2_HUMAN 17-125 B D | cellular tumor antigen P53 | P53_HUMAN 15-29 Non-standard residues in 4hfz.pdb #4 --- SO4 — sulfate ion > open /Users/maryam/Downloads/4hg7.pdb 4hg7.pdb title: Crystal structure of an MDM2/nutlin-3A complex [more info...] Chain information for 4hg7.pdb #7 --- Chain | Description | UniProt A | E3 ubiquitin-protein ligase MDM2 | MDM2_HUMAN 17-108 Non-standard residues in 4hg7.pdb #7 --- NUT — 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one (nutlin 3A) SO4 — sulfate ion 46 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/maryam/Downloads/6i3s.pdb 6i3s.pdb title: Crystal structure of MDM2 In complex with compound 13. [more info...] Chain information for 6i3s.pdb #8 --- Chain | Description | UniProt A | E3 ubiquitin-protein ligase MDM2 | MDM2_HUMAN 18-111 Non-standard residues in 6i3s.pdb #8 --- GOL — glycerol (glycerin; propane-1,2,3-triol) H28 — (3~{S},3'~{R},3'~{A}~{S},6'~{A}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl- phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{A},6~{A}-dihydro-3~{H}-pyrrolo[3,4-B]pyrrole]-2,4'-dione SO4 — sulfate ion 22 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/maryam/Downloads/6k3f.pdb 6k3f.pdb title: Crystal structure of β-arrestin 2 In complex with CXCR7 phosphopeptide [more info...] Chain information for 6k3f.pdb #9 --- Chain | Description | UniProt A B C D E F | arrestin β-2 | ARRB2_RAT 1-356 U V W X Y Z | peptide from atypical chemokine receptor 3 | ACKR3_HUMAN 331-345 > open /Users/maryam/Downloads/8goc.pdb 8goc.pdb title: Structure of β-ARRESTIN2 In complex with A phosphopeptide corresponding to the human vasopressin V2 receptor, V2R [more info...] Chain information for 8goc.pdb #10 --- Chain | Description | UniProt A B C | β-arrestin-2 | ARRB2_BOVIN 1-420 D H M | FAB30 heavy chain | E L N | FAB30 light chain | G U V | vasopressin V2 receptor | V2R_HUMAN 343-371 > hide #4 models > show #4 models > select add #9 17278 atoms, 17111 bonds, 2 pseudobonds, 2630 residues, 3 models selected > select subtract #9 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #9 17278 atoms, 17111 bonds, 2 pseudobonds, 2630 residues, 3 models selected > select subtract #9 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > close #9 > hide #!10 models > show #!10 models > close #10 > ui tool show Matchmaker > matchmaker #2-4,7-8#!1 to #5 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 fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with 1rv1.pdb, chain C (#2), sequence alignment score = 35.9 RMSD between 14 pruned atom pairs is 1.528 angstroms; (across all 83 pairs: 16.069) Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with 1ycr.pdb, chain A (#3), sequence alignment score = 31.6 RMSD between 12 pruned atom pairs is 1.257 angstroms; (across all 78 pairs: 15.063) Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with 4hfz.pdb, chain C (#4), sequence alignment score = 29.3 RMSD between 14 pruned atom pairs is 1.338 angstroms; (across all 84 pairs: 15.804) Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with 4hg7.pdb, chain A (#7), sequence alignment score = 29.8 RMSD between 13 pruned atom pairs is 1.233 angstroms; (across all 85 pairs: 15.415) Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with 6i3s.pdb, chain A (#8), sequence alignment score = 16 RMSD between 11 pruned atom pairs is 0.785 angstroms; (across all 94 pairs: 20.863) Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with 8hsv.pdb, chain E (#1), sequence alignment score = 16.6 RMSD between 4 pruned atom pairs is 1.484 angstroms; (across all 15 pairs: 12.815) > zoom 3 > hide #!1 models > hide #2 models > hide #3 models > hide #4 models > hide #5 models > show #4 models > show #3 models > show #5 models > hide #4 models > hide #3 models > hide #7 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > open ""/Users/maryam/Downloads/fold_bai1_wt_2024_06_01_10_49 > 2/fold_bai1_wt_2024_06_01_10_49_model_0.cif"" Chain information for fold_bai1_wt_2024_06_01_10_49_model_0.cif #9 --- Chain | Description A | . > ui tool show Matchmaker > matchmaker #9 to #8 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 6i3s.pdb, chain A (#8) with fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment score = 28 RMSD between 16 pruned atom pairs is 0.909 angstroms; (across all 77 pairs: 16.729) > hide #9 models > show #9 models > hide #9 models > show #9 models > hide #9 models > hide #5 models > hide #8 models > show #9 models > ui tool show ""Show Sequence Viewer"" > sequence chain #9/A Alignment identifier is 9/A > select #9/A:928 7 atoms, 6 bonds, 1 residue, 1 model selected > select #9/A:181-928 5723 atoms, 5860 bonds, 748 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/A:1206 4 atoms, 3 bonds, 1 residue, 1 model selected > select #9/A:1206-1584 2918 atoms, 3007 bonds, 379 residues, 1 model selected > select #9/A:1207 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:1207-1210 26 atoms, 25 bonds, 4 residues, 1 model selected > select #9/A:1206 4 atoms, 3 bonds, 1 residue, 1 model selected > select #9/A:1206-1584 2918 atoms, 3007 bonds, 379 residues, 1 model selected > select #9/A:1540-1584 360 atoms, 368 bonds, 45 residues, 1 model selected > select #9/A:1207-1584 2914 atoms, 3003 bonds, 378 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:1-180 1385 atoms, 1425 bonds, 180 residues, 1 model selected > delete atoms sel > delete bonds sel > show #8 models > show #5 models > ui tool show Matchmaker > matchmaker #5,7#!9 to #8 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 6i3s.pdb, chain A (#8) with fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment score = 16 RMSD between 11 pruned atom pairs is 0.785 angstroms; (across all 94 pairs: 20.863) Matchmaker 6i3s.pdb, chain A (#8) with 4hg7.pdb, chain A (#7), sequence alignment score = 434.4 RMSD between 83 pruned atom pairs is 0.742 angstroms; (across all 91 pairs: 1.240) Matchmaker 6i3s.pdb, chain A (#8) with fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment score = 16 RMSD between 11 pruned atom pairs is 1.015 angstroms; (across all 94 pairs: 21.177) > hide #!9 models > show #!9 models > hide #5 models > select #9/A:971 6 atoms, 5 bonds, 1 residue, 1 model selected > select #9/A:971 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > select #5/A:971 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:971 8 atoms, 7 bonds, 1 residue, 1 model selected > show #5 models > show sel target ab > tile 3 models tiled > select clear > select #9/A:971 6 atoms, 5 bonds, 1 residue, 1 model selected > select #9/A:971 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel yellow > ui tool show Matchmaker > matchmaker #5,7#!9 to #8 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 6i3s.pdb, chain A (#8) with fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment score = 16 RMSD between 11 pruned atom pairs is 0.785 angstroms; (across all 94 pairs: 20.863) Matchmaker 6i3s.pdb, chain A (#8) with 4hg7.pdb, chain A (#7), sequence alignment score = 434.4 RMSD between 83 pruned atom pairs is 0.742 angstroms; (across all 91 pairs: 1.240) Matchmaker 6i3s.pdb, chain A (#8) with fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment score = 16 RMSD between 11 pruned atom pairs is 1.015 angstroms; (across all 94 pairs: 21.177) > hide #5 models > hide #!9 models > ui tool show Matchmaker > matchmaker #!9 to #8 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 6i3s.pdb, chain A (#8) with fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment score = 16 RMSD between 11 pruned atom pairs is 1.015 angstroms; (across all 94 pairs: 21.177) > show #!9 models > move y -100 > move y +20 > move y +5 > hbonds sel reveal true 2 hydrogen bonds found > hbonds sel reveal true 2 hydrogen bonds found > select #8/A:111 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:107 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:107-111 38 atoms, 37 bonds, 5 residues, 1 model selected > select #8/A:111 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:18-111 774 atoms, 789 bonds, 94 residues, 1 model selected > select sel : hbonds sel & #8#!9 reveal true 606 hydrogen bonds found > open /Users/maryam/Downloads/7wcn.pdb 7wcn.pdb title: Cryo-em structure of GPR119-GS complex with small molecule agonist AR231453 [more info...] Chain information for 7wcn.pdb #10 --- Chain | Description | UniProt A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394 B | transducin β chain 1 | GBB1_HUMAN 13-351 C | G γ-I | GBG2_HUMAN 1-71 N | NB35 | R | G-protein coupled receptor 119 | GP119_HUMAN 1-335 Non-standard residues in 7wcn.pdb #10 --- 8WL — N-(2-fluoranyl-4-methylsulfonyl- phenyl)-5-nitro-6-[4-(3-propan-2-yl-1,2,4-oxadiazol-5-yl)piperidin-1-yl]pyrimidin-4-amine (AR231453) > hide #!9 models > hide #8 models > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8217 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > ui tool show ""Show Sequence Viewer"" > show #!9 models > show #5 models > ui tool show Matchmaker > matchmaker #5,7-8#!9 to #10 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7wcn.pdb, chain R (#10) with fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment score = 268.8 RMSD between 56 pruned atom pairs is 0.940 angstroms; (across all 258 pairs: 8.524) Matchmaker 7wcn.pdb, chain A (#10) with 4hg7.pdb, chain A (#7), sequence alignment score = 36.9 RMSD between 6 pruned atom pairs is 1.405 angstroms; (across all 68 pairs: 19.462) Matchmaker 7wcn.pdb, chain A (#10) with 6i3s.pdb, chain A (#8), sequence alignment score = 31.4 RMSD between 9 pruned atom pairs is 0.409 angstroms; (across all 79 pairs: 17.047) Matchmaker 7wcn.pdb, chain R (#10) with fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment score = 271.6 RMSD between 55 pruned atom pairs is 0.883 angstroms; (across all 258 pairs: 8.528) > hide #5 models > ui tool show ""Show Sequence Viewer"" > sequence chain #10/A Alignment identifier is 10/A > sequence chain #10/B Alignment identifier is 10/B > sequence chain #10/C Alignment identifier is 10/C > sequence chain #10/N Alignment identifier is 10/N > select clear > select #10/N 973 atoms, 994 bonds, 128 residues, 1 model selected > delete atoms sel > delete bonds sel > select #10/B:351 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/B:46-351 2346 atoms, 2393 bonds, 306 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > delete atoms #6,9-10 > delete bonds #6,9-10 > open /Users/maryam/Downloads/7wcn.pdb 7wcn.pdb title: Cryo-em structure of GPR119-GS complex with small molecule agonist AR231453 [more info...] Chain information for 7wcn.pdb #9 --- Chain | Description | UniProt A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394 B | transducin β chain 1 | GBB1_HUMAN 13-351 C | G γ-I | GBG2_HUMAN 1-71 N | NB35 | R | G-protein coupled receptor 119 | GP119_HUMAN 1-335 Non-standard residues in 7wcn.pdb #9 --- 8WL — N-(2-fluoranyl-4-methylsulfonyl- phenyl)-5-nitro-6-[4-(3-propan-2-yl-1,2,4-oxadiazol-5-yl)piperidin-1-yl]pyrimidin-4-amine (AR231453) > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8217 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > select #9/B:13-351 2606 atoms, 2653 bonds, 339 residues, 1 model selected > sequence chain #9/B Alignment identifier is 9/B > select #9/B:351 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/B 2606 atoms, 2653 bonds, 339 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/N:1-128 973 atoms, 994 bonds, 128 residues, 1 model selected > sequence chain #9/N Alignment identifier is 9/N > select clear > select #9/N 973 atoms, 994 bonds, 128 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/A:9-394 1947 atoms, 1983 bonds, 2 pseudobonds, 235 residues, 2 models selected > sequence chain #9/A Alignment identifier is 9/A > sequence chain #9/B Chains must have same sequence > select #9/B:13-351 Nothing selected > select #9/B:13-351 Nothing selected > sequence chain #9/B Chains must have same sequence > sequence chain #9/C Alignment identifier is 9/C > select clear > select #9/C 451 atoms, 457 bonds, 58 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select #9/A:9-286 1048 atoms, 1062 bonds, 2 pseudobonds, 127 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #9/A Destroying pre-existing alignment with identifier 9/A Alignment identifier is 9/A > sequence chain #9/R Alignment identifier is 9/R > select clear > select #9/R:5-300 2240 atoms, 2295 bonds, 1 pseudobond, 289 residues, 2 models selected > delete atoms (#!9 & sel) > delete bonds (#!9 & sel) > select clear > sequence chain #9/B Chains must have same sequence > select add #9/R:401@C26 1 atom, 13 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select add #9/R:401@O6 1 atom, 1 residue, 1 model selected > select add #9/R:401@C8 2 atoms, 1 residue, 1 model selected > select add #9/R:401@C1 3 atoms, 1 residue, 1 model selected > select add #9/R:401@C16 4 atoms, 4 bonds, 1 residue, 1 model selected > select add #9/R:401@O24 5 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@C23 6 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@O25 7 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@O31 8 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@N30 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@O32 10 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@C3 11 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@C10 12 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@C4 13 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@C9 14 atoms, 8 bonds, 1 residue, 1 model selected > select add #9/R:401@N5 15 atoms, 9 bonds, 1 residue, 1 model selected > select add #9/R:401@C14 16 atoms, 9 bonds, 1 residue, 1 model selected > select add #9/R:401@C29 17 atoms, 9 bonds, 1 residue, 1 model selected > select add #9/R:401@C27 18 atoms, 9 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select add #9/R:401@C20 1 atom, 1 residue, 1 model selected > select add #9/R:401@C19 2 atoms, 1 residue, 1 model selected > select add #9/R:401@C33 3 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@C34 4 atoms, 1 bond, 1 residue, 1 model selected > select subtract #9/R:401@C34 3 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@C34 4 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@C7 5 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@N35 6 atoms, 1 bond, 1 residue, 1 model selected > select subtract #9/R:401@C7 5 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@C7 6 atoms, 1 bond, 1 residue, 1 model selected > select subtract #9/R:401@N35 5 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@C2 6 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@N13 7 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@C12 8 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@F28 9 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@N15 10 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@N11 11 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@N17 12 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@C18 13 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@C21 14 atoms, 1 bond, 1 residue, 1 model selected > select add #9/R:401@S22 15 atoms, 1 bond, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select add #9/R:401@N35 1 atom, 1 residue, 1 model selected > delete atoms sel > delete bonds sel ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8rc202405170741 (2024-05-17) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AX00298LL/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 13 hours, 49 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 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: 2023.11.17 cftime: 1.6.3 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 ChimeraX-AtomicLibrary: 14.0.5 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: 1.2.4 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-ColorActions: 1.0.4 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: 1.8rc202405170741 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: 1.2.3 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-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 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 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: 1.13.4 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-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: 3.0.3 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: 1.16.4 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 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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 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: 4.51.0 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: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 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: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 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 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 setuptools-scm: 8.0.4 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 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX