id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14597 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.6-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 Thread 0x000070001ef66000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001bf5d000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001cf60000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007000186c5000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000112204600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py"", line 576 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 1613 in remove_deleted_pointers File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 134 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 894 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 253 in filter File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 813 in selected_items File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/selection.py"", line 46 in items File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/select.py"", line 170 in report_selection File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/select.py"", line 62 in select 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/seq_view/region_browser.py"", line 1763 in _select_on_structures File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/region_browser.py"", line 1585 in _mouse_up_cb 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, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, 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COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 308K 38 \nColorSync 232K 28 \nCoreAnimation 416K 34 \nCoreGraphics 12K 2 \nCoreServices 876K 3 \nCoreUI image data 5156K 38 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 549.5M 730 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 24K 6 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 128K 32 \nStack 243.8M 33 \nStack Guard 56.0M 1 \nVM_ALLOCATE 179.6M 222 \n__CTF 756 1 \n__DATA 47.0M 688 \n__DATA_CONST 32.6M 345 \n__DATA_DIRTY 1641K 212 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 678.5M 162 \n__TEXT 816.8M 688 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 493.4M 80 \nshared memory 2980K 26 \n=========== ======= ======= \nTOTAL 3.3G 3401 \nTOTAL, minus reserved VM space 3.0G 3401 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000361 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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 > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23 > CRAMP1 SANT domain residues mutagenesis/NPAT_CR1_full_SANT.cxs"" format > session opened ChimeraX session > ui tool show ""AlphaFold Error Plot"" > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_11/best_model.pdb Chain information for best_model.pdb #2 --- Chain | Description A | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B Alignment identifier is 1/B > color sel bynucleotide > select add #1 5621 atoms, 5724 bonds, 36 pseudobonds, 739 residues, 2 models selected > color sel bynucleotide Alignment identifier is 1/A Destroying pre-existing alignment with identifier 1/B Alignment identifier is 1/B > select #1/B:22 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:22 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:4-5 13 atoms, 12 bonds, 2 residues, 1 model selected > select #1/B:4-70 579 atoms, 596 bonds, 67 residues, 1 model selected > select #1/B:2 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/B:2 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/B:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:5-61 489 atoms, 502 bonds, 57 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2 to #1 & sel 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 best_model.pdb, chain B (#1) with best_model.pdb, chain A (#2), sequence alignment score = 312 RMSD between 57 pruned atom pairs is 0.314 angstroms; (across all 57 pairs: 0.314) > select #1/A:563 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:563-589 197 atoms, 197 bonds, 27 residues, 1 model selected > select #1/A:563-589,658-664 254 atoms, 254 bonds, 34 residues, 1 model selected > select #1/A:668 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:650-668 150 atoms, 154 bonds, 19 residues, 1 model selected > select #1/A:660-661 20 atoms, 20 bonds, 2 residues, 1 model selected > select #1/A:660-661 20 atoms, 20 bonds, 2 residues, 1 model selected > select #1/A:661 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:661 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:665 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:665 8 atoms, 7 bonds, 1 residue, 1 model selected > save ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/2024 2 12 > CRAMP1 DUF UBL mutants/DUF_SANT_align.cxs"" > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb Chain information for best_model.pdb #3 --- Chain | Description A | No description available B | No description available > hide #3 models > hide #2 models > hide #!1 models > select add #1 5621 atoms, 5724 bonds, 36 pseudobonds, 739 residues, 2 models selected > select subtract #1 Nothing selected > hide #1.1 models > show #3 models > color #3 bychain > close #3 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb Chain information for best_model.pdb #3 --- Chain | Description A | No description available B | No description available > color #3 bychain > show #!1 models > ui tool show Matchmaker > select #1/B:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:5-17 112 atoms, 114 bonds, 13 residues, 1 model selected > select #1/B:4-5 13 atoms, 12 bonds, 2 residues, 1 model selected > select #1/B:4-62 504 atoms, 517 bonds, 59 residues, 1 model selected > select #1/B:3-4 20 atoms, 21 bonds, 2 residues, 1 model selected > select #1/B:3-62 518 atoms, 533 bonds, 60 residues, 1 model selected > ui tool show Matchmaker > matchmaker #3 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 best_model.pdb, chain B (#1) with best_model.pdb, chain B (#3), sequence alignment score = 380.8 RMSD between 70 pruned atom pairs is 0.754 angstroms; (across all 70 pairs: 0.754) > show #2 models > hide #2 models > hide #!1 models > show #!1 models Destroying pre-existing alignment with identifier 1/B Alignment identifier is 1/B Destroying pre-existing alignment with identifier 1/B Alignment identifier is 1/B > select #1/A:55 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:55 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:658 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:658 7 atoms, 6 bonds, 1 residue, 1 model selected Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > ui tool show ""Show Sequence Viewer"" > close #3 > hide #!1 models > show #2 models > hide #2 models > show #!1 models > hide #!1 models > show #!1 models > close #1 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color #1 bychain > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > select #1/A:26 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:26 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:33 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:33 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:1 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:1 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:1 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:1-30 232 atoms, 234 bonds, 30 residues, 1 model selected > close #1 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_7/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color #1 bychain > close #1 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_8/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color #1 bychain > close #1 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_9/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color #1 bychain > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/B Alignment identifier is 1/B > select #1/A:17 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:17 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:5-11 59 atoms, 59 bonds, 7 residues, 1 model selected > select #1/B:23 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:23-24 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/B:76 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:76 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:84 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:84 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:88 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/B:88 4 atoms, 3 bonds, 1 residue, 1 model selected > close #1 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_10/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color #1 bychain > close #1 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_11/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available > color #1 bychain > close #1 > close > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23 > CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color bychain Alignment identifier is 1/A Alignment identifier is 1/B > select /B:11 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:11 11 atoms, 11 bonds, 1 residue, 1 model selected > hide #1 models > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_7/best_model.pdb Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > color #2 bychain > hide #2 target m > close #2 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > color #2 bychain Alignment identifier is 1/B > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:1 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A 261 atoms, 263 bonds, 33 residues, 1 model selected > close #2 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > color #2 bychain > close #2 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_8/best_model.pdb Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > color #2 bychain > close #2 > show #1 models > select /B:6 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:6-8 26 atoms, 25 bonds, 3 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:658 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:658 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:563-564 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:532-563 233 atoms, 239 bonds, 32 residues, 1 model selected > select /A:658 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:658-664 57 atoms, 57 bonds, 7 residues, 1 model selected > select /A:665-666 18 atoms, 18 bonds, 2 residues, 1 model selected > select /A:665-666 18 atoms, 18 bonds, 2 residues, 1 model selected > select /A:658 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:658-665 65 atoms, 65 bonds, 8 residues, 1 model selected > select /A:669 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:662-669 69 atoms, 70 bonds, 8 residues, 1 model selected > select /A:639 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:639-669 254 atoms, 259 bonds, 31 residues, 1 model selected > select /A:669 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:648-669 174 atoms, 179 bonds, 22 residues, 1 model selected > select /A:639-640 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:639-643 44 atoms, 43 bonds, 5 residues, 1 model selected > select /A:669 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:648-669 174 atoms, 179 bonds, 22 residues, 1 model selected > ui tool show AlphaFold > alphafold predict > LPSSFPAGMDVDKFLLSLHYDE,ESWSTEDKNTFFEGLYEHGKDFEAIQNNIALKYKKKGKPASMVKNKEQVRHFYYRTWHKITKYIDFD Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction > close AlphaFold prediction finished Results in /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_12 > open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_12/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color bychain > alphafold pae #1 file > /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_12/best_model_pae.json > alphafold contacts Missing or invalid ""residues"" argument: empty atom specifier > alphafold contacts /AA No residues specified for alphafold contacts > alphafold contacts /A Alignment identifier is 1/A Alignment identifier is 1/B > select /A:15 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:15 8 atoms, 7 bonds, 1 residue, 1 model selected > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23 > CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model.pdb"" Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > ui tool show Matchmaker > select #1/B:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:5-67 545 atoms, 560 bonds, 63 residues, 1 model selected > select #1/B:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:5-67 545 atoms, 560 bonds, 63 residues, 1 model selected > 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 best_model.pdb, chain B (#1) with best_model.pdb, chain B (#2), sequence alignment score = 362.2 RMSD between 66 pruned atom pairs is 0.528 angstroms; (across all 67 pairs: 0.627) > color sel bychain > hide #!1 models > color #2 bychain > alphafold contacts /A /B Interface PAE pseudobonds can only be computed for a single structure, got 2. > select add #1 754 atoms, 776 bonds, 12 pseudobonds, 89 residues, 2 models selected > select subtract #1 Nothing selected > alphafold contacts /A /B Interface PAE pseudobonds can only be computed for a single structure, got 2. > close #1 > close > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23 > CRAMP1 SANT domain residues > mutagenesis/AlphaFold/prediction_11/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available > close > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23 > CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm_short/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color bychain > alphafold pae #1 file ""/Users/enaden/Documents/Cambridge Year 4/Part III > Project/3_10_23 CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm_short/best_model_pae.json"" > alphafold contacts /A /B Alignment identifier is 1/A Alignment identifier is 1/B > select /B:12 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:12 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:16 12 atoms, 12 bonds, 1 residue, 1 model selected > select /B:16-17 21 atoms, 21 bonds, 2 pseudobonds, 2 residues, 2 models selected > select /B:54 12 atoms, 12 bonds, 1 residue, 1 model selected > select /B:54 12 atoms, 12 bonds, 1 residue, 1 model selected > select /B:53 12 atoms, 12 bonds, 1 residue, 1 model selected > select /B:53 12 atoms, 12 bonds, 1 residue, 1 model selected > select /B:56 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:56 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:60 8 atoms, 7 bonds, 1 residue, 1 model selected > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23 > CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model.pdb"" Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > hide #!1 models > color #2 bychain > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file ""/Users/enaden/Documents/Cambridge Year 4/Part III > Project/3_10_23 CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model_pae.json"" Number of residues in structure ""best_model.pdb #1"" is 89 which does not match PAE matrix size 739. This can happen if chains were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error. > alphafold pae #1 file ""/Users/enaden/Documents/Cambridge Year 4/Part III > Project/3_10_23 CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model_pae.json"" Number of residues in structure ""best_model.pdb #1"" is 89 which does not match PAE matrix size 739. This can happen if chains were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error. > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file ""/Users/enaden/Documents/Cambridge Year 4/Part III > Project/3_10_23 CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model_pae.json"" > alphafold contacts /A /B Interface PAE pseudobonds can only be computed for a single structure, got 2. > close #1 > alphafold contacts /A /B Alignment identifier is 2/A Alignment identifier is 2/B > select /B:12 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:12 11 atoms, 11 bonds, 1 residue, 1 model selected > select /B:53 12 atoms, 12 bonds, 1 residue, 1 model selected > select /B:53 12 atoms, 12 bonds, 1 residue, 1 model selected > select /B:56 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:56 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:60 8 atoms, 7 bonds, 1 residue, 1 model selected > close #2 > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23 > CRAMP1 SANT domain residues > mutagenesis/AlphaFold/SANT_NPAT_Cterm_short/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > color bychain > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/2024 2 12 > CRAMP1 DUF UBL mutants/DUF_NPAT_Cterm/best_model.pdb"" Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > close #2 > open ""/Users/enaden/Documents/Cambridge Year 4/Part III Project/2024 2 12 > CRAMP1 DUF UBL mutants/DUF/best_model.pdb"" Chain information for best_model.pdb #2 --- Chain | Description A | No description available Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 2/A > select #1/B:4-5 13 atoms, 12 bonds, 2 residues, 1 model selected > select #1/B:4-61 ===== 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 INTEL-18.8.5 OpenGL renderer: Intel(R) UHD Graphics 617 OpenGL vendor: Intel 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: MacBook Air Model Identifier: MacBookAir8,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6 (21G115) Kernel Version: Darwin 21.6.0 Time since boot: 17 days 19:00 Graphics/Displays: Intel UHD Graphics 617: Chipset Model: Intel UHD Graphics 617 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x87c0 Revision ID: 0x0002 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) 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-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-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 can't reproduce Tom Goddard all ChimeraX