id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19788 Crash in find_close_points chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 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 0x00000001f1956c40 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1487 in apply_auto_styling File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 206 in added_to_session File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1385 in added_to_session File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py"", line 827 in add File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 297 in provider_open File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3237 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 132 in cmd_open File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3237 in run File ""/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 355 in _qt_safe File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 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, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, 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TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 ColorSync 80K 5 CoreAnimation 1248K 68 CoreGraphics 96K 5 CoreUI image data 3456K 25 Foundation 48K 2 Kernel Alloc Once 32K 1 MALLOC 651.5M 156 MALLOC guard page 3664K 4 Mach message 64K 3 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 912K 57 Stack 202.9M 58 Stack Guard 56.0M 1 VM_ALLOCATE 221.2M 117 VM_ALLOCATE (reserved) 352.0M 1 reserved VM address space (unallocated) __AUTH 5816K 641 __AUTH_CONST 88.2M 1028 __CTF 824 1 __DATA 42.9M 1113 __DATA_CONST 59.0M 1160 __DATA_DIRTY 8673K 887 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 621.1M 128 __OBJC_RO 78.4M 1 __OBJC_RW 2570K 1 __TEXT 1.4G 1111 __TEXT (graphics) 68.1M 71 __TPRO_CONST 128K 2 dyld private memory 432K 5 mapped file 334.0M 56 page table in kernel 1394K 1 shared memory 3728K 26 =========== ======= ======= TOTAL 4.1G 6745 TOTAL, minus reserved VM space 3.8G 6745 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""6870681ebb16e536f5c56233a6306dbf3936fe37"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""trmStatus"" : 2048, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""66d35d7fe4d6bf7664f40ddf"", ""factorPackIds"" : [ ""68c1a34bd359577bbe8f2182"" ], ""deploymentId"" : 240000068 }, { ""rolloutId"" : ""68095e8ecb2a9d1eaa8463c9"", ""factorPackIds"" : [ ""68bf4eacb556ea03e19aed49"" ], ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/vivekadarsh/Downloads/4JX3.pdb 4JX3.pdb title: Crystal structure of PIM1 kinase [more info...] Chain information for 4JX3.pdb #1 --- Chain | Description | UniProt A | PIM1 kinase | PIM1_HUMAN 1-313 > set bgColor white > lighting full > show cartoons > hide cartoons > show cartoons > open /Users/vivekadarsh/Downloads/4JX3.pdb 4JX3.pdb title: Crystal structure of PIM1 kinase [more info...] Chain information for 4JX3.pdb #2 --- Chain | Description | UniProt A | PIM1 kinase | PIM1_HUMAN 1-313 > open /Users/vivekadarsh/Downloads/PIM1/251121094721-2ef9a718_cmpx.pdb > /Users/vivekadarsh/Downloads/PIM1/251121101614-a628c515_cmpx.pdb > /Users/vivekadarsh/Downloads/PIM1/251121102040-36a71612_cmpx.pdb > /Users/vivekadarsh/Downloads/PIM1/251121103201-eb44cdb8_cmpx.pdb > /Users/vivekadarsh/Downloads/PIM1/251121103852-1c15afa8_cmpx.pdb > /Users/vivekadarsh/Downloads/PIM1/251121110540-941bf4a5_cmpx.pdb Summary of feedback from opening /Users/vivekadarsh/Downloads/PIM1/251121094721-2ef9a718_cmpx.pdb --- warnings | Ignored bad PDB record found on line 2228 REMARK VINA RESULT: -12.2 0.000 0.000 Ignored bad PDB record found on line 2229 REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34 Ignored bad PDB record found on line 2230 REMARK SMILES O=C(c1cc2c(=O)[nH]ccc2c(N2CCOc3ccccc3C2)n1)c1ccccc1C(=O)N1CCCC1 Ignored bad PDB record found on line 2231 REMARK SMILES IDX 25 1 26 2 27 3 28 4 29 5 30 6 2 7 1 8 3 9 4 10 24 11 5 12 Ignored bad PDB record found on line 2232 REMARK SMILES IDX 12 13 6 14 11 15 8 16 10 17 9 18 7 19 13 21 14 22 23 23 3 messages similar to the above omitted notes | Combining 110 symmetry atoms into GLN /A:285 CG Combining 31 symmetry atoms into GLN /A:285 NE2 Combining 33 symmetry atoms into GLN /A:285 O Summary of feedback from opening /Users/vivekadarsh/Downloads/PIM1/251121101614-a628c515_cmpx.pdb --- warnings | Ignored bad PDB record found on line 2228 REMARK VINA RESULT: -12.2 0.000 0.000 Ignored bad PDB record found on line 2229 REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34 Ignored bad PDB record found on line 2230 REMARK SMILES O=C(c1ccc2c(c1)CNCC2)c1cc2c(=O)[nH]ccc2c(N2CCOc3ccccc3C2)n1 Ignored bad PDB record found on line 2231 REMARK SMILES IDX 1 1 2 2 3 3 4 4 8 5 5 6 7 7 6 8 9 9 12 10 10 11 11 12 13 14 Ignored bad PDB record found on line 2232 REMARK SMILES IDX 14 15 34 16 15 17 22 18 16 19 21 20 18 21 20 22 19 23 17 24 3 messages similar to the above omitted notes | /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py:519: RuntimeWarning: overflow encountered in cast xyzr[:, :3] = atoms.coords Combining 6 symmetry atoms into GLN /A:285 CG Combining 3 symmetry atoms into GLN /A:285 NE2 Combining 4 symmetry atoms into GLN /A:285 O Combining 2 symmetry atoms into HIS /A:287 CD2 Combining 3 symmetry atoms into GLN /A:291 NE2 Combining 4 symmetry atoms into PRO /A:296 CG Combining 4 symmetry atoms into ASP /A:292 CG Combining 5 symmetry atoms into MET /A:290 CA Combining 2 symmetry atoms into TRP /A:289 CG Combining 5 symmetry atoms into MET /A:290 C Combining 3 symmetry atoms into GLN /A:297 O Combining 2 symmetry atoms into TRP /A:289 C Combining 2 symmetry atoms into THR /A:299 CB Summary of feedback from opening /Users/vivekadarsh/Downloads/PIM1/251121102040-36a71612_cmpx.pdb --- warnings | Ignored bad PDB record found on line 2228 REMARK VINA RESULT: -11.9 0.000 0.000 Ignored bad PDB record found on line 2229 REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34 Ignored bad PDB record found on line 2230 REMARK SMILES O=C1C[C@@H](c2cccc(-c3cc4c(=O)[nH]ccc4c(N4CCOc5ccccc5C4)n3)c2)CN1 Ignored bad PDB record found on line 2231 REMARK SMILES IDX 5 1 6 2 7 3 8 4 9 5 32 6 4 7 2 8 3 9 34 10 33 11 1 12 10 14 Ignored bad PDB record found on line 2232 REMARK SMILES IDX 11 15 31 16 12 17 19 18 13 19 18 20 15 21 17 22 16 23 14 24 3 messages similar to the above omitted notes | Combining 110 symmetry atoms into GLN /A:285 CG Combining 31 symmetry atoms into GLN /A:285 NE2 Combining 33 symmetry atoms into GLN /A:285 O Summary of feedback from opening /Users/vivekadarsh/Downloads/PIM1/251121103201-eb44cdb8_cmpx.pdb --- warnings | Ignored bad PDB record found on line 2228 REMARK VINA RESULT: -12.0 0.000 0.000 Ignored bad PDB record found on line 2229 REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34 Ignored bad PDB record found on line 2230 REMARK SMILES O=C1CC[C@@H]2COc3ccc(Cc4cc5c(=O)[nH]ccc5c(N5CCOc6ccccc6C5)n4)cc3N12 Ignored bad PDB record found on line 2231 REMARK SMILES IDX 12 1 11 2 2 3 3 4 37 5 4 6 5 7 36 8 6 9 8 10 35 11 7 12 9 13 Ignored bad PDB record found on line 2232 REMARK SMILES IDX 10 14 1 15 13 16 14 17 34 18 15 19 22 20 16 21 21 22 18 23 3 messages similar to the above omitted Some X/Y/Z coordinate values in the '251121103201-eb44cdb8_cmpx.pdb' PDB file are not finite numbers > open /Users/vivekadarsh/Downloads/PIM1/251121103852-1c15afa8_cmpx.pdb Summary of feedback from opening /Users/vivekadarsh/Downloads/PIM1/251121103852-1c15afa8_cmpx.pdb --- warnings | Ignored bad PDB record found on line 2228 REMARK VINA RESULT: -12.4 0.000 0.000 Ignored bad PDB record found on line 2229 REMARK CORE O=c3[nH]ccc4c(N2CCOc1ccccc1C2)nc([*:1])cc34 Ignored bad PDB record found on line 2230 REMARK SMILES CN1CCc2cc(C(=O)c3cc4c(=O)[nH]ccc4c(N4CCOc5ccccc5C4)n3)ccc2C1 Ignored bad PDB record found on line 2231 REMARK SMILES IDX 8 1 9 2 7 3 2 4 3 5 35 6 4 7 34 8 5 9 33 10 6 11 32 12 1 13 Ignored bad PDB record found on line 2232 REMARK SMILES IDX 10 14 11 15 31 16 12 17 19 18 13 19 18 20 15 21 17 22 16 23 3 messages similar to the above omitted notes | Combining 1381 symmetry atoms into TYR /A:38 CA Combining 380 symmetry atoms into GLN /A:37 NE2 Combining 394 symmetry atoms into GLN /A:37 OE1 Combining 8 symmetry atoms into MET /A:88 SD Chain information for 251121103852-1c15afa8_cmpx.pdb #3 --- Chain | Description A | No description available /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py:1607: RuntimeWarning: invalid value encountered in subtract lv = translation(center - radius * ld) * orthonormal_frame(-ld) /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py:972: RuntimeWarning: invalid value encountered in scalar add return (d-r, d+r) /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/camera.py:254: RuntimeWarning: invalid value encountered in subtract bc = bounds.box_corners() - center /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/camera.py:259: RuntimeWarning: invalid value encountered in multiply camera_center = center - d*view_direction /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/camera.py:259: RuntimeWarning: invalid value encountered in subtract camera_center = center - d*view_direction /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/geometry/matrix.py:177: RuntimeWarning: invalid value encountered in scalar multiply \+ m1[r][2] * m2[2][c]) /Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/geometry/matrix.py:176: RuntimeWarning: invalid value encountered in scalar multiply p[r][c] = (m1[r][0] * m2[0][c] + m1[r][1] * m2[1][c] > open /Users/vivekadarsh/Downloads/PIM1/251123220754-33c69291-7_cmpx.pdb Summary of feedback from opening /Users/vivekadarsh/Downloads/PIM1/251123220754-33c69291-7_cmpx.pdb --- warnings | Ignored bad PDB record found on line 2484 REMARK VINA RESULT: -11.842 0.000 0.000 Ignored bad PDB record found on line 2485 REMARK INTER + INTRA: -14.445 Ignored bad PDB record found on line 2486 REMARK INTER: -14.265 Ignored bad PDB record found on line 2487 REMARK INTRA: -0.180 Ignored bad PDB record found on line 2488 REMARK UNBOUND: -0.180 5 messages similar to the above omitted notes | Combining 11 symmetry atoms into GLN /A:140 CG Combining 2 symmetry atoms into ARG /A:122 NH1 Combining 15 symmetry atoms into ILE /A:133 O Combining 789 symmetry atoms into GLN /A:37 CA Combining 209 symmetry atoms into GLN /A:37 NE2 Combining 472 symmetry atoms into SER /A:36 O Combining 6 symmetry atoms into MET /A:88 SD Combining 2 symmetry atoms into PHE /A:281 C Combining 2 symmetry atoms into LYS /A:67 O Combining 3 symmetry atoms into VAL /A:69 C Combining 3 symmetry atoms into LYS /A:71 CB Combining 2 symmetry atoms into ASP /A:239 N Combining 4 symmetry atoms into VAL /A:69 CG1 Combining 2 symmetry atoms into GLU /A:79 OE2 Combining 5 symmetry atoms into LEU /A:62 CB Combining 2 symmetry atoms into LEU /A:107 N Combining 3 symmetry atoms into LYS /A:71 CE Combining 3 symmetry atoms into VAL /A:64 CG2 Combining 2 symmetry atoms into GLY /A:162 CA Combining 3 symmetry atoms into ARG /A:73 CZ Combining 2 symmetry atoms into LEU /A:92 O Combining 4 symmetry atoms into PRO /A:113 CD Combining 2 symmetry atoms into ASN /A:160 ND2 Combining 10 symmetry atoms into PHE /A:116 O Combining 2 symmetry atoms into ILE /A:213 CG1 Combining 2 symmetry atoms into ILE /A:119 N ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M4 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,6 Model Number: Z1FG000AVLL/A Chip: Apple M4 Max Total Number of Cores: 16 (12 performance and 4 efficiency) Memory: 128 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 2 days, 9 hours, 16 minutes Graphics/Displays: Apple M4 Max: Chipset Model: Apple M4 Max Type: GPU Bus: Built-In Total Number of Cores: 40 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 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: 1.11.1 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: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 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-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 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: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Core limitation Eric Pettersen all ChimeraX