id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18474 ChimeraX bug report submission goddard@… "{{{ The following bug report has been submitted: Platform: macOS-15.6-arm64-arm-64bit ChimeraX Version: 1.11.dev202508140657 (2025-08-14 06:57:21 UTC) Description Last time you used ChimeraX it crashed. I had the Side View shown and it was floating and I clicked the side view close window button on the title bar and ChimeraX crashed. This is the PySide tech preview ChimeraX build. Fatal Python error: Segmentation fault Thread 0x000000046efef000 (most recent call first): File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000464837000 (most recent call first): File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 566 in select File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 1898 in _run_once File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 608 in run_forever File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tornado/platform/asyncio.py"", line 211 in start File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/iostream.py"", line 92 in _thread_main File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000046382b000 (most recent call first): File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 327 in wait File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py"", line 1110 in run File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py"", line 98 in only_when_enabled File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/decorator.py"", line 235 in fun File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000428667000 (most recent call first): File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Users/goddard/Library/Application Support/ChimeraX/1.11/lib/python/site-packages/tqdm/_monitor.py"", line 60 in run File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00000001f73b60c0 (most recent call first): File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1058 in init File ""/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1223 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, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, shiboken6.Shiboken, PySide6.QtCore, PySide6.QtGui, PySide6.QtWidgets, PySide6.QtNetwork, 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\nPROTECTED_MEMORY 16K 1 \nSTACK GUARD 57.4M 89 \nStack 288.9M 89 \nVM_ALLOCATE 664.0M 807 \nVM_ALLOCATE (reserved) 1.4G 6 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 40.2M 1306 \n__DATA_CONST 63.3M 1296 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 684.0M 349 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.5G 1317 \n__TEXT (graphics) 352K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 28.1M 188 \nmapped file 629.5M 87 \npage table in kernel 2731K 1 \nshared memory 3296K 26 \n=========== ======= ======= \nTOTAL 10.0G 8046 \nTOTAL, minus reserved VM space 8.6G 8046 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""28f42922aa61bf67b7398c44b1a0240cfab7923f"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000218 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.dev202508140657 (2025-08-14) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1tw7 format mmcif fromDatabase pdb 1tw7 title: Wide Open 1.3A Structure of a Multi-drug Resistant HIV-1 Protease Represents a Novel Drug Target [more info...] Chain information for 1tw7 #1 --- Chain | Description A B | protease Non-standard residues in 1tw7 #1 --- NA — sodium ion 54 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 1890 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > ui tool show Boltz > boltz predict protein /A protein /B ligandCcd NA(2) name 1tw7 Running Boltz prediction of protein with 198 residues, 2 ligands NA (2) on gpu Using cached multiple sequence alignment /Users/goddard/Downloads/ChimeraX/BoltzMSA/1tw7_msa Confidence score 0.96, pTM 0.97, ipTM 0.96 (ligand 0.94, protein 0.96), pLDDT 0.96 Boltz prediction completed in 47 seconds (start boltz 4 sec, sequence search 0 sec, load weights 11 sec, structure inference 33 sec) Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these predictions. > open /Users/goddard/Desktop/boltz/boltz_1tw7_6/1tw7_model_0.cif logInfo > false Matchmaker 1tw7, chain A (#1) with 1tw7_model_0.cif, chain A (#2), sequence alignment score = 496.9 RMSD between 99 pruned atom pairs is 0.382 angstroms; (across all 99 pairs: 0.382) > boltz predict protein #1/A protein #1/B ligandSmiles > CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)C4=CC=C(C=C4)N > name 1tw7 affinity > CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)C4=CC=C(C=C4)N Running Boltz prediction of protein with 198 residues, 1 ligands CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)C4=CC=C(C=C4)N on gpu Using cached multiple sequence alignment /Users/goddard/Downloads/ChimeraX/BoltzMSA/1tw7_msa > ui tool show ""Similar Structures"" > foldseek #1/A Found 409 similar structures to 1tw7 #1/A in pdb database using foldseek, name fs1 > open 3omh Summary of feedback from opening 3omh fetched from pdb --- note | Fetching compressed mmCIF 3omh from http://files.rcsb.org/download/3omh.cif 3omh title: Crystal structure of PTPN22 in complex with SKAP-HOM pTyr75 peptide [more info...] Chain information for 3omh #3 --- Chain | Description | UniProt A B C D | Tyrosine-protein phosphatase non-receptor type 22 | PTN22_HUMAN 1-294 E F G H | Src kinase-associated phosphoprotein 2 | SKAP2_HUMAN 390-398 3omh mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly Deleted 7 extra chains, 102 C-terminal residues, 169 N-terminal residues, 139 non-polymer residues more than 3.0 Angstroms away. Alignment of 3omh chain C to query has RMSD 0.852 using 9 of 23 paired residues within cutoff distance 2.0 > open 6nir Summary of feedback from opening 6nir fetched from pdb --- note | Fetching compressed mmCIF 6nir from http://files.rcsb.org/download/6nir.cif 6nir title: Crystal structure of a GII.4 norovirus HOV protease [more info...] Chain information for 6nir #4 --- Chain | Description A B C D | HOV protease X | HOV protease fragment 6nir mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 5209 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Deleted 4 extra chains, 34 C-terminal residues, 47 N-terminal residues. Alignment of 6nir chain D to query has RMSD 1.27 using 8 of 70 paired residues within cutoff distance 2.0 > similarstructures traces 409 backbone traces > similarstructures cluster #1/A:27,86,26,52,66 clusterDistance 1.5 Clustered 320 of 409 hits that have the specified 5 residues into 5 groups Confidence score 0.92, pTM 0.98, ipTM 0.97 (ligand 0.97, protein 0.98), pLDDT 0.91 Ligand CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)C4=CC=C(C=C4)N predicted binding affinity 0.091 uM, predicted binding probability 0.82 Boltz prediction completed in 122 seconds (start boltz 3 sec, sequence search 0 sec, load weights 11 sec, structure inference 36 sec, load affinity weights 11 sec, affinity inference 61 sec) > open /Users/goddard/Desktop/boltz/boltz_1tw7_7/1tw7_model_0.cif logInfo > false Matchmaker 1tw7, chain A (#1) with 1tw7_model_0.cif, chain A (#6), sequence alignment score = 504.1 RMSD between 99 pruned atom pairs is 0.404 angstroms; (across all 99 pairs: 0.404) > hide #!3 models > hide #6 models > hide #!5 models > hide #4 models > hide #2 models > open 3bxr Summary of feedback from opening 3bxr fetched from pdb --- notes | Fetching compressed mmCIF 3bxr from http://files.rcsb.org/download/3bxr.cif Fetching CCD DRR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/DRR/DRR.cif 3bxr title: Crystal Structures Of Highly Constrained Substrate And Hydrolysis Products Bound To HIV-1 Protease. Implications For Catalytic Mechanism [more info...] Chain information for 3bxr #7 --- Chain | Description | UniProt A B | Protease | POL_HV1A2 1-99 101-199 Non-standard residues in 3bxr #7 --- DRR — (9S,12S)-9-(1-methylethyl)-N-[(8S,11S)-8-[(1S)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]-7,10-dioxo-2-oxa-8,11-diazabicyclo[12.2.2]octadeca-1(16),14,17-triene-12-carboxamide SO4 — sulfate ion 58 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Hit structure sequence 3bxr_B amino acid A at sequence position 66 does not match sequence alignment G at position 66. Structure sequence PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF. Alignment sequence PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEIGHKAIGTVLVGPTPVNIIGRNLLTQIGTLNF. Deleted 1 extra chains, 2 C-terminal residues, 140 non-polymer residues more than 3.0 Angstroms away. Alignment of 3bxr chain B to query has RMSD 0.796 using 56 of 97 paired residues within cutoff distance 2.0 > show #!3 models > show #6 models > hide #!3 models > hide #3.1 models > show #3.1 models > hide #3.1 models > show #3.1 models > hide #3.1 models > show #3.1 models > hide #3.1 models > show #3.1 models > select subtract #3.1 Nothing selected > select add #3.1 Nothing selected > show #1,6-7#!3 atoms > select subtract #3.1 Nothing selected > select add #3.1 Nothing selected > select #3 206 atoms, 209 bonds, 24 residues, 1 model selected > open 1080 format ccp4 fromDatabase emdb Opened emdb 1080 as #8, grid size 100,100,100, pixel 2.7, shown at level 0.852, step 1, values float32 > volume #8 level 1.657 > volume #8 style image > volume #8 level -0.0001241,0 level 1.675,0.8 level 2.365,1 > volume #8 step 2 > volume #8 step 1 > ui tool show ""Fit Loops"" Populating font family aliases took 163 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > ui tool show ""Side View"" > ui tool show Shell > ui windowfill toggle > ui tool show ""Color Actions"" > color sel #ff666dff > color sel #ff666dfc > color sel #ff666ded > color sel #ff666de0 > color sel #ff666dd7 > color sel #ff666dcd > color sel #ff666dc7 > color sel #ff666dbd > color sel #ff666db5 > color sel #ff666db0 > color sel #ff666dac > color sel #ff666da7 > color sel #ff666da5 > color sel #ff666da3 > color sel #ff666da1 > color sel #ff666d9b > color sel #ff666d97 > color sel #ff666d91 > color sel #ff666d8e > color sel #ff666d8a > color sel #ff666d88 > color sel #ff666d85 > color sel #ff666d82 > color sel #ff666d81 > color sel #ff666d80 > color sel #ff666d73 > color sel #ff666d60 > color sel #ff666d56 > color sel #ff666d42 > color sel #ff666d37 > color sel #ff666d27 > color sel #ff666d1f > color sel #ff666d15 > color sel #ff666d11 > color sel #ff666d10 > color sel #ff666d0e > color sel #ff666d0d > color sel #ff666d0c > color sel #ff666d0b > color sel #ff666d0c > color sel #ff666d0d > color sel #ff666d0e > color sel #ff666d0f > color sel #ff666d10 > color sel #ff666d16 > color sel #ff666d1a > color sel #ff666d20 > color sel #ff666d30 > color sel #ff666d40 > color sel #ff666d4a > color sel #ff666d51 > color sel #ff666d54 > color sel #ff666d59 > color sel #ff666d5b > color sel #ff666d5f > color sel #ff666d64 > color sel #ff666d66 > color sel #ff666d67 > color sel #ff666d68 > color sel #ff666d67 > color sel #ff666d61 > color sel #ff666d5d > color sel #ff666d57 > color sel #ff666d54 > color sel #ff666d4a > color sel #ff666d43 > color sel #ff666d35 > color sel #ff666d2e > color sel #ff666d22 > color sel #ff666d1d > color sel #ff666d15 > color sel #ff666d12 > color sel #ff666d11 > color sel #ff666d14 > color sel #ff666d1a > color sel #ff666d24 > color sel #ff666d2b > color sel #ff666d3f > color sel #ff666d54 > color sel #ff666d61 > color sel #ff666d77 > color sel #ff666d87 > color sel #ff666d8f > color sel #ff666d96 > color sel #ff666d9a > color sel #ff666d9c > color sel #ff666d9f > color sel #ff666da1 > color sel #ff666da6 > color sel #ff666da9 > color sel #ff666daf > color sel #ff666db4 > color sel #ff666dbd > color sel #ff666dc6 > color sel #ff666dcc > color sel #ff666dd4 > color sel #ff666dde > color sel #ff666de1 > color sel #ff666dea > color sel #ff666df1 > color sel #ff666df6 > color sel #ff666df9 > color sel #ff666dff > color sel #ff666dee > color sel #ff666de1 > color sel #ff666dcd > color sel #ff666dbd > color sel #ff666db7 > color sel #ff666dae > color sel #ff666da9 > color sel #ff666da6 > color sel #ff666da5 > color sel #ff666da6 > color sel #ff666da7 > color sel #ff666da8 > color sel #ff666dad > color sel #ff666db9 > color sel #ff666dc5 > color sel #ff666ddf > color sel #ff666df2 > color sel #ff666dff > ui mousemode right tug Missing atoms or parameterization needed by force field. All heavy atoms and hydrogens with standard names are required. Error with ignoreExternalBonds=False was No template found for residue 1 (ILE). The set of atoms is similar to HID, but it is missing 9 atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template Error with ignoreExternalBonds=True was No template found for residue 1 (ILE). The set of atoms is similar to HID, but it is missing 9 atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template > ui mousemode right label > label #3/C:192 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.dev202508140657 (2025-08-14) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 Ultra OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PySide6 6.9.1, Qt 6.9.1 Qt runtime version: 6.9.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac14,14 Model Number: Z1800003VLL/A Chip: Apple M2 Ultra Total Number of Cores: 24 (16 performance and 8 efficiency) Memory: 64 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6 (24G84) Kernel Version: Darwin 24.6.0 Time since boot: 10 days, 21 hours, 54 minutes Graphics/Displays: Apple M2 Ultra: Chipset Model: Apple M2 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 278B1: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.4 blockdiag: 3.0.0 blosc2: 3.7.1 build: 1.2.2.post1 certifi: 2025.7.14 cftime: 1.6.4.post1 charset-normalizer: 3.4.3 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.0.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.12 ChimeraX-AtomicLibrary: 14.1.22 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.dev202508140657 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.17 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.5.1 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: 1.0.1 ChimeraX-MutationScores: 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: 1.15.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.3.8 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.4 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.4 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.2 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.48.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.10.4 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.2 debugpy: 1.8.16 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.1 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.30.1 ipython: 9.4.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.7 jedi: 0.19.2 Jinja2: 3.1.6 joblib: 1.5.0 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.9 line_profiler: 5.0.0 llvmlite: 0.44.0 lxml: 5.3.1 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.2 matplotlib: 3.10.3 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numba: 0.61.2 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynndescent: 0.5.13 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PySide6: 6.9.1 PySide6_Addons: 6.9.1 PySide6_Essentials: 6.9.1 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.1 qtconsole: 5.6.1 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 requests: 2.32.4 roman-numerals-py: 3.1.0 scikit-learn: 1.6.1 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 shiboken6: 6.9.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.5 tables: 3.10.2 tcia_utils: 1.5.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.2 tqdm: 4.67.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 umap-learn: 0.5.7 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect new normal Unassigned