id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15359 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.4.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff845189640 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py"", line 81 in msgpack_deserialize File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 721 in restore File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1017 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 484 in remember_data_format File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 514 in collated_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 213 in provider_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 131 in cmd_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 334 in _qt_safe File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, 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2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/johncowgill/Desktop/a5b3/ApoLMNG/Autosharpen_1/Apo.ccp4 format > ccp4 Opened Apo.ccp4 as #1, grid size 440,440,440, pixel 0.65, shown at level 1.94, step 2, values float32 > open > /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde_real_space_refined_011.cif Summary of feedback from opening /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde_real_space_refined_011.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 346 Missing entity information. Treating each chain as a separate entity. Atom H is not in the residue template for ASP /A:8 Atom H is not in the residue template for ASN /D:11 Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 29064 Skipping chem_comp category: Missing column 'type' near line 29252 Skipping chem_comp category: Missing column 'type' near line 29395 Skipping chem_comp category: Missing column 'type' near line 29509 Skipping chem_comp category: Missing column 'type' near line 29697 1 messages similar to the above omitted Chain information for isolde_real_space_refined_011.cif #2 --- Chain | Description A | No description available B C | No description available D | No description available E | No description available > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 141 residues in model #2 to IUPAC-IUB standards. Chain information for isolde_real_space_refined_011.cif --- Chain | Description 2.2/A | No description available 2.2/B 2.2/C | No description available 2.2/D | No description available 2.2/E | No description available > clipper associate #1 toModel #2 Opened Apo.ccp4 as #2.1.1.1, grid size 440,440,440, pixel 0.65, shown at step 1, values float32 > volume #2.1.1.1 level 4.676 > select #2.2/D:122 24 atoms, 23 bonds, 1 residue, 1 model selected > view sel > delete atoms (#!2.2 & sel) > delete bonds (#!2.2 & sel) > ui tool show ""Add Hydrogens"" > addh #!2.2 Summary of feedback from adding hydrogens to isolde_real_space_refined_011.cif #2.2 --- notes | No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain A; guessing termini instead No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain B; guessing termini instead No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain C; guessing termini instead No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain D; guessing termini instead No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain E; guessing termini instead Chain-initial residues that are actual N termini: /B PRO 6, /C PRO 6, /E PRO 6 Chain-initial residues that are not actual N termini: /A ASP 8, /A ALA 320, /B GLU 549, /C GLU 549, /D ASN 11, /D ALA 320, /E LYS 552 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ARG 352, /A PRO 317, /B SER 584, /B GLN 309, /C SER 584, /C GLN 309, /D ARG 352, /D GLN 316, /E SER 584, /E SER 308 1529 hydrogen bonds /A ARG 352 is not terminus, removing H atom from 'C' /B SER 584 is not terminus, removing H atom from 'C' /C SER 584 is not terminus, removing H atom from 'C' /D ARG 352 is not terminus, removing H atom from 'C' /E SER 584 is not terminus, removing H atom from 'C' 3 hydrogens added > select #2.2/D:276 24 atoms, 23 bonds, 1 residue, 1 model selected > view sel > select clear > volume #2.1.1.1 level 2.033 > select clear > save /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde.cif > relModel #2.2 Not saving entity_poly_seq for non-authoritative sequences > select #2.2/D:276 24 atoms, 23 bonds, 1 residue, 1 model selected > view sel > save /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde.cif > relModel #2.2 Not saving entity_poly_seq for non-authoritative sequences > select #2.2/D:122 24 atoms, 23 bonds, 1 residue, 1 model selected > view sel > ui tool show ""Build Structure"" > select clear > select add #2.2 28440 atoms, 28833 bonds, 60 pseudobonds, 1737 residues, 12 models selected > isolde sim start /A,D-E,C,B,Z Loading residue template for BUA from internal database Loading residue template for EPE from internal database Sim termination reason: None ISOLDE: stopped sim Deleted the following atoms from residue EPE B610: H1, H4 > isolde sim start /B:610 ISOLDE: started sim > select clear > select #2.2/D:122 24 atoms, 23 bonds, 1 residue, 1 model selected > view sel > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #2.2 28438 atoms, 28831 bonds, 60 pseudobonds, 1737 residues, 17 models selected > isolde sim start /A,D-E,C,B,Z ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 21 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde.cif > relModel #2.2 Not saving entity_poly_seq for non-authoritative sequences > close session > open > /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/isolde_real_space_refined_012.cif Summary of feedback from opening /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/isolde_real_space_refined_012.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 252 Missing entity information. Treating each chain as a separate entity. Atom H is not in the residue template for ASP /A:8 Atom H is not in the residue template for ASN /D:11 Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 28970 Skipping chem_comp category: Missing column 'type' near line 29158 Skipping chem_comp category: Missing column 'type' near line 29301 Skipping chem_comp category: Missing column 'type' near line 29489 Skipping chem_comp category: Missing column 'type' near line 29603 1 messages similar to the above omitted Chain information for isolde_real_space_refined_012.cif #1 --- Chain | Description A | No description available B C | No description available D | No description available E | No description available ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 143 residues in model #1 to IUPAC-IUB standards. Chain information for isolde_real_space_refined_012.cif --- Chain | Description 1.2/A | No description available 1.2/B 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available > open /Users/johncowgill/Desktop/a5b3/ApoLMNG/Autosharpen_1/Apo.ccp4 Opened Apo.ccp4 as #2, grid size 440,440,440, pixel 0.65, shown at level 1.94, step 2, values float32 > clipper associate #2 toModel #1 Opened Apo.ccp4 as #1.1.1.1, grid size 440,440,440, pixel 0.65, shown at step 1, values float32 > select #1.2/A:94 11 atoms, 10 bonds, 1 residue, 1 model selected > view sel > volume #1.1.1.1 level 2.837 > select #1.2/D:61 15 atoms, 14 bonds, 1 residue, 1 model selected > view sel > select #1.2/E:43 12 atoms, 11 bonds, 1 residue, 1 model selected > view sel > save > /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif > relModel #1.2 Not saving entity_poly_seq for non-authoritative sequences > close session > open > /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif Summary of feedback from opening /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif --- warnings | Unknown polymer entity '1' near line 226 Unknown polymer entity '2' near line 5834 Unknown polymer entity '3' near line 17437 Unknown polymer entity '4' near line 22943 Atom H is not in the residue template for ASP /A:8 Atom H is not in the residue template for ASN /D:11 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for Resting_Final.cif #1 --- Chain | Description A | No description available B C | No description available D | No description available E | No description available > hide atoms > show cartoons > measure buriedarea #4/B:1-220 withAtoms2 #4/C:1-220 Buried area between #4/B:1-220 and #4/C:1-220 = 0 area #4/B:1-220 = 0, area #4/C:1-220 = 0, area both = 0 > measure buriedarea #1/B:1-220 withAtoms2 #1/C:1-220 Buried area between #1/B:1-220 and #1/C:1-220 = 1242.7 area #1/B:1-220 = 12270, area #1/C:1-220 = 12442, area both = 22226 > measure buriedarea #1/B:1-220 withAtoms2 #1/A:1-220 Buried area between #1/B:1-220 and #1/A:1-220 = 1351.9 area #1/B:1-220 = 12270, area #1/A:1-220 = 12126, area both = 21692 > measure buriedarea #1/C:1-220 withAtoms2 #1/A:1-220 Buried area between #1/C:1-220 and #1/A:1-220 = 0 area #1/C:1-220 = 12442, area #1/A:1-220 = 12126, area both = 24568 > measure buriedarea #1/E:1-220 withAtoms2 #1/A:1-220 Buried area between #1/E:1-220 and #1/A:1-220 = 1446.1 area #1/E:1-220 = 12371, area #1/A:1-220 = 12126, area both = 21605 > measure buriedarea #1/D:1-220 withAtoms2 #1/E:1-220 Buried area between #1/D:1-220 and #1/E:1-220 = 1421.1 area #1/D:1-220 = 12301, area #1/E:1-220 = 12371, area both = 21830 > measure buriedarea #1/C:1-220 withAtoms2 #1/D:1-220 Buried area between #1/C:1-220 and #1/D:1-220 = 1537.4 area #1/C:1-220 = 12442, area #1/D:1-220 = 12301, area both = 21668 > measure buriedarea #1/B:1-220 withAtoms2 #1/C:1-220 Buried area between #1/B:1-220 and #1/C:1-220 = 1242.7 area #1/B:1-220 = 12270, area #1/C:1-220 = 12442, area both = 22226 > open /Users/johncowgill/Desktop/a5b3/GABAbound.pdb Summary of feedback from opening /Users/johncowgill/Desktop/a5b3/GABAbound.pdb --- warning | Ignored bad PDB record found on line 1 Chain information for GABAbound.pdb #2 --- Chain | Description A | No description available B C | No description available D | No description available E | No description available P | No description available > measure buriedarea #2/B:1-220 withAtoms2 #2/C:1-220 Buried area between #2/B:1-220 and #2/C:1-220 = 1425.2 area #2/B:1-220 = 12366, area #2/C:1-220 = 12477, area both = 21993 > measure buriedarea #2/B:1-220 withAtoms2 #2/A:1-220 Buried area between #2/B:1-220 and #2/A:1-220 = 1553.6 area #2/B:1-220 = 12366, area #2/A:1-220 = 12523, area both = 21781 > measure buriedarea #2/B:1-220 withAtoms2 #2/C:1-220 Buried area between #2/B:1-220 and #2/C:1-220 = 1425.2 area #2/B:1-220 = 12366, area #2/C:1-220 = 12477, area both = 21993 > measure buriedarea #2/D:1-220 withAtoms2 #2/C:1-220 Buried area between #2/D:1-220 and #2/C:1-220 = 1539.2 area #2/D:1-220 = 12298, area #2/C:1-220 = 12477, area both = 21697 > measure buriedarea #2/D:1-220 withAtoms2 #2/E:1-220 Buried area between #2/D:1-220 and #2/E:1-220 = 1551.4 area #2/D:1-220 = 12298, area #2/E:1-220 = 12371, area both = 21566 > measure buriedarea #2/D:E:220-588 withAtoms2 #2/E:220-588 Buried area between #2/D:E:220-588 and #2/E:220-588 = 952.67 area #2/D:E:220-588 = 10144, area #2/E:220-588 = 7926.2, area both = 16165 > measure buriedarea #1/D:E:220-588 withAtoms2 #1/E:220-588 Buried area between #1/D:E:220-588 and #1/E:220-588 = 1330.7 area #1/D:E:220-588 = 9759.6, area #1/E:220-588 = 7861.4, area both = 14960 > measure buriedarea #1/D:E withAtoms2 #1/E Buried area between #1/D:E and #1/E = 0 area #1/D:E = 0, area #1/E = 19864, area both = 19864 > measure buriedarea #1/D withAtoms2 #1/E Buried area between #1/D and #1/E = 2840.3 area #1/D = 19253, area #1/E = 19864, area both = 33436 > measure buriedarea #1/D:E:220-588 withAtoms2 #1/E:220-588 Buried area between #1/D:E:220-588 and #1/E:220-588 = 1330.7 area #1/D:E:220-588 = 9759.6, area #1/E:220-588 = 7861.4, area both = 14960 > measure buriedarea #1/D:E:1-220 withAtoms2 #1/E:1-220 Buried area between #1/D:E:1-220 and #1/E:1-220 = 1421.1 area #1/D:E:1-220 = 12301, area #1/E:1-220 = 12371, area both = 21830 > measure buriedarea #1/D:E:1-588 withAtoms2 #1/E:1-588 Buried area between #1/D:E:1-588 and #1/E:1-588 = 2830.7 area #1/D:E:1-588 = 19253, area #1/E:1-588 = 18712, area both = 32304 > measure buriedarea #1/D:1-588 withAtoms2 #1/E:1-588 Buried area between #1/D:1-588 and #1/E:1-588 = 2830.7 area #1/D:1-588 = 19253, area #1/E:1-588 = 18712, area both = 32304 > hide atoms > show cartoons > hide #!1 models > select > ::name=""ABU""::name=""BMA""::name=""BUA""::name=""EPE""::name=""MAN""::name=""NAG""::name=""ZN"" 1839 atoms, 1884 bonds, 77 residues, 2 models selected > show (#!2 & sel) target ab > select up 51665 atoms, 52363 bonds, 3167 residues, 2 models selected > measure buriedarea #1/D:E:1-588 withAtoms2 #1/E:1-588 Buried area between #1/D:E:1-588 and #1/E:1-588 = 2830.7 area #1/D:E:1-588 = 19253, area #1/E:1-588 = 18712, area both = 32304 > measure buriedarea #1/D:1-588 withAtoms2 #1/E:1-588 Buried area between #1/D:1-588 and #1/E:1-588 = 2830.7 area #1/D:1-588 = 19253, area #1/E:1-588 = 18712, area both = 32304 > measure buriedarea #1/D:1-219 withAtoms2 #1/E:1-219 Buried area between #1/D:1-219 and #1/E:1-219 = 1421.1 area #1/D:1-219 = 12358, area #1/E:1-219 = 12172, area both = 21688 > measure buriedarea #1/D:220-588 withAtoms2 #1/E:220-588 Buried area between #1/D:220-588 and #1/E:220-588 = 1330.7 area #1/D:220-588 = 9759.6, area #1/E:220-588 = 7861.4, area both = 14960 > measure buriedarea #1/B:1-219 withAtoms2 #1/C:1-219 Buried area between #1/B:1-219 and #1/C:1-219 = 1242.7 area #1/B:1-219 = 12074, area #1/C:1-219 = 12294, area both = 21883 > measure buriedarea #1/B:1-219 withAtoms2 #1/C:1-584 Buried area between #1/B:1-219 and #1/C:1-584 = 1372.2 area #1/B:1-219 = 12074, area #1/C:1-584 = 19189, area both = 28519 > measure buriedarea #1/B:1-584 withAtoms2 #1/C:1-584 Buried area between #1/B:1-584 and #1/C:1-584 = 2692.4 area #1/B:1-584 = 18858, area #1/C:1-584 = 19189, area both = 32663 > measure buriedarea #1/B:1-219 withAtoms2 #1/C:1-219 Buried area between #1/B:1-219 and #1/C:1-219 = 1242.7 area #1/B:1-219 = 12074, area #1/C:1-219 = 12294, area both = 21883 > measure buriedarea #1/B:219-585 withAtoms2 #1/C:219-585 Buried area between #1/B:219-585 and #1/C:219-585 = 1351.2 area #1/B:219-585 = 8159, area #1/C:219-585 = 8374.7, area both = 13831 > measure buriedarea #1/B:220-585 withAtoms2 #1/C:220-585 Buried area between #1/B:220-585 and #1/C:220-585 = 1349.1 area #1/B:220-585 = 8131.7, area #1/C:220-585 = 8351.6, area both = 13785 > measure buriedarea #1/B:220-585 withAtoms2 #1/C:1-220 Buried area between #1/B:220-585 and #1/C:1-220 = 0 area #1/B:220-585 = 8131.7, area #1/C:1-220 = 12442, area both = 20573 > measure buriedarea #1/C:220-585 withAtoms2 #1/B:1-220 Buried area between #1/C:220-585 and #1/B:1-220 = 230.99 area #1/C:220-585 = 8351.6, area #1/B:1-220 = 12270, area both = 20159 > close session > open /Users/johncowgill/Desktop/a5b3/SapGABALong/map/refine201.mrc format > mrc Opened refine201.mrc as #1, grid size 440,440,440, pixel 0.648, shown at level 0.000503, step 2, values float32 > volume #1 level 0.0008984 > volume #1 level 0.001109 > close session > open /Users/johncowgill/Desktop/a5b3/ECDoverlay.cxs Opened refine201.mrc as #2, grid size 440,440,440, pixel 0.648, shown at level 0.000978, step 2, values float32 opened ChimeraX session > ui tool show ""Side View"" > show (sel-residues & sidechain) target ab > style sel stick Changed 48 atom styles > color sel byhetero > select H 42627 atoms, 5218 residues, 3 models selected > delete atoms (#!1,4 & sel) > delete bonds (#!1,4 & sel) > select #1/B:ABU 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel target ab > color sel byhetero > cofr showPivot false > view sel > select clear > show sel atoms > style sel stick Changed 14 atom styles > color sel byhetero > select #1/B:ABU 7 atoms, 6 bonds, 1 residue, 1 model selected > style sel ball Changed 7 atom styles > style sel stick Changed 18 atom styles > show sel atoms > color sel byhetero > view sel > graphics silhouettes width1 Expected true or false or a keyword > graphics silhouettes width 1 > select clear > style sel stick Changed 24 atom styles > show sel atoms > color sel byhetero > select up 116 atoms, 118 bonds, 14 residues, 2 models selected > select up 5162 atoms, 5305 bonds, 626 residues, 2 models selected > select up 5180 atoms, 5321 bonds, 628 residues, 2 models selected > select down 5162 atoms, 5305 bonds, 626 residues, 2 models selected > select clear > select #4/B:BUA 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel stick Changed 6 atom styles > show sel atoms > style sel ball Changed 6 atom styles > color sel byhetero > style sel stick Changed 22 atom styles > show sel atoms > select ~sel & ##selected 28553 atoms, 29340 bonds, 10 pseudobonds, 3479 residues, 5 models selected > select #1,4 28575 atoms, 29362 bonds, 10 pseudobonds, 3481 residues, 5 models selected > transparency sel 20 > transparency sel 20 ribbons > select clear > ui tool show Distances > distance #4/B:202@CB #1/B:202@CB Distance between ApoA5B3-coot-0.pdb #4/B THR 202 CB and isolde_real_space_refined_018.pdb #1/B THR 202 CB: 1.714Å > select clear > hide #!5 models > hide #5.1 models > open > /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif Summary of feedback from opening /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif --- warnings | Unknown polymer entity '1' near line 226 Unknown polymer entity '2' near line 5834 Unknown polymer entity '3' near line 17437 Unknown polymer entity '4' near line 22943 Atom H is not in the residue template for ASP /A:8 Atom H is not in the residue template for ASN /D:11 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for Resting_Final.cif #6 --- Chain | Description A | No description available B C | No description available D | No description available E | No description available > hide #!1,4,6 atoms > show #!1,4,6 cartoons > select #6/A:1-222 3401 atoms, 3442 bonds, 215 residues, 1 model selected > ui tool show Matchmaker > matchmaker #6/A & sel to #4/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ApoA5B3-coot-0.pdb, chain A (#4) with Resting_Final.cif, chain A (#6), sequence alignment score = 1112.8 RMSD between 215 pruned atom pairs is 0.097 angstroms; (across all 215 pairs: 0.097) > select #6/A:1-222 3401 atoms, 3442 bonds, 215 residues, 1 model selected > ui tool show Matchmaker > matchmaker #6/A & sel to #1/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker isolde_real_space_refined_018.pdb, chain A (#1) with Resting_Final.cif, chain A (#6), sequence alignment score = 1104.4 RMSD between 211 pruned atom pairs is 0.638 angstroms; (across all 215 pairs: 0.723) > select #6/A:BUA Nothing selected > select #6/B:BUA 13 atoms, 12 bonds, 1 residue, 1 model selected > show sel target ab > select H 28375 atoms, 3474 residues, 2 models selected > delete atoms (#!6 & sel) > delete bonds (#!6 & sel) > hide #!4 models > show sel target ab > style sel stick Changed 36 atom styles > color sel byhetero > show sel target ab > style sel stick Changed 42 atom styles > color sel byhetero > select #1/B:ABU 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #6/A:BUA Nothing selected > style #!1,6 ball Changed 28536 atom styles > undo > select #6/A:BUA Nothing selected > select #6/B:BUA 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel ball Changed 6 atom styles > color #1 #929292ff > color sel byhetero > select #1 14280 atoms, 14676 bonds, 4 pseudobonds, 1739 residues, 2 models selected > color (#!1 & sel) byhetero > select #6/B:1-590 2785 atoms, 2860 bonds, 1 pseudobond, 340 residues, 2 models selected > color sel #882255 > color (#!6 & sel) byhetero > select #6/A:1-450 2817 atoms, 2891 bonds, 1 pseudobond, 348 residues, 2 models selected > color sel #DDCC77 > color (#!6 & sel) byhetero > select up 14256 atoms, 14649 bonds, 5 pseudobonds, 1737 residues, 2 models selected > select up 14256 atoms, 14649 bonds, 8 pseudobonds, 1737 residues, 3 models selected > select #6/B:BUA 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #DDCC77 > color sel byhetero > select clear > show sel target ab > style sel stick Changed 22 atom styles > hide sel atoms > open > /Users/johncowgill/Desktop/a5b3/LMNGGABA/RealSpaceRefine_11/isolde_real_space_refined_011.pdb Chain information for isolde_real_space_refined_011.pdb #7 --- Chain | Description A | No description available B C | No description available D | No description available E | No description available P | No description available > hide sel atoms > show sel cartoons > select add #7 30323 atoms, 30721 bonds, 5 pseudobonds, 1861 residues, 4 models selected > hide sel atoms > show sel cartoons > select #6/A:1-222 1725 atoms, 1766 bonds, 215 residues, 1 model selected > select #7/A:1-222 3401 atoms, 3442 bonds, 215 residues, 1 model selected > ui tool show Matchmaker > matchmaker #7/A & sel to #1/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker isolde_real_space_refined_018.pdb, chain A (#1) with isolde_real_space_refined_011.pdb, chain A (#7), sequence alignment score = 1071.4 RMSD between 214 pruned atom pairs is 0.419 angstroms; (across all 215 pairs: 0.457) > select #7/B:ABU 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel target ab > hide #!7 models > show #!7 models > close session > open /Volumes/KINGSTON/Fig1/Fig1.cxs ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.12.7 OpenGL renderer: AMD Radeon Pro 570 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac18,3 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3,4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 24 GB System Firmware Version: 512.0.0.0.0 OS Loader Version: 577~170 SMC Version (system): 2.41f2 Software: System Software Overview: System Version: macOS 13.4.1 (22F82) Kernel Version: Darwin 22.5.0 Time since boot: 9 days, 21 hours, 21 minutes Graphics/Displays: Radeon Pro 570: Chipset Model: Radeon Pro 570 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c5 ROM Revision: 113-D000AA-931 VBIOS Version: 113-D0001A1L-025 EFI Driver Version: 01.00.931 Metal Support: Metal 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) 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: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 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: 1.7.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate all ChimeraX