id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20456 msa3d not skipping None residues kklee@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.12.dev202604220250 (2026-04-22 02:50:42 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.12.dev202604220250 (2026-04-22) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 2C36 fromDatabase pdb format mmcif Summary of feedback from opening 2C36 fetched from pdb --- note | Fetching compressed mmCIF 2c36 from http://files.rcsb.org/download/2c36.cif 2c36 title: Structure of unliganded HSV gD reveals a mechanism for receptor- mediated activation of virus entry [more info...] Chain information for 2c36 #1 --- Chain | Description | UniProt A B | GLYCOPROTEIN D HSV-1 | VGLD_HHV1P 23-307 Non-standard residues in 2c36 #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CL — chloride ion MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) ZN — zinc ion 2c36 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 12 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 3U82 fromDatabase pdb format mmcif Summary of feedback from opening 3U82 fetched from pdb --- note | Fetching compressed mmCIF 3u82 from http://files.rcsb.org/download/3u82.cif 3u82 title: Binding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell adhesion [more info...] Chain information for 3u82 #2 --- Chain | Description | UniProt A | Envelope glycoprotein D | GD_HHV11 1-285 B | Poliovirus receptor-related protein 1 | PVRL1_HUMAN 30-335 14 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 4164 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > ui mousemode right ""translate selected models"" > select add #2 4164 atoms, 4276 bonds, 531 residues, 1 model selected Drag select of 1 residues > select add #2 4173 atoms, 4276 bonds, 532 residues, 2 models selected > view matrix models > #1,1,0,0,3.4063,0,1,0,-3.5384,0,0,1,-15.333,#2,1,0,0,3.4063,0,1,0,-3.5384,0,0,1,-15.333 > view matrix models > #1,1,0,0,1.9236,0,1,0,-2.2865,0,0,1,-14.648,#2,1,0,0,1.9236,0,1,0,-2.2865,0,0,1,-14.648 Drag select of 38 residues > select add #2 4164 atoms, 4276 bonds, 531 residues, 1 model selected > view matrix models #2,1,0,0,10.913,0,1,0,-5.4823,0,0,1,72.473 > select clear > select add #2 4164 atoms, 4276 bonds, 531 residues, 1 model selected > view matrix models #2,1,0,0,49.396,0,1,0,10.72,0,0,1,74.14 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.36377,0.23781,0.90062,93.031,0.2102,0.92097,-0.32808,-4.3201,-0.90746,0.30866,0.28503,95.517 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.36377,0.23781,0.90062,60.161,0.2102,0.92097,-0.32808,39.017,-0.90746,0.30866,0.28503,92.057 > select #2/B 2350 atoms, 2405 bonds, 300 residues, 1 model selected > select #1/B 2378 atoms, 2211 bonds, 1 pseudobond, 511 residues, 2 models selected > cartoon hide (#!1 & sel) > hide (#!1 & sel) target a Drag select of 61 atoms, 63 bonds > hide sel target a Drag select of 15 atoms, 13 bonds Drag select of 17 atoms, 15 bonds > hide sel target a > select add #1 4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected > view matrix models #1,1,0,0,-1.9223,0,1,0,-10.557,0,0,1,-11.522 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.9967,0.07801,-0.022516,-2.9128,-0.077916,0.99695,0.005019,-6.3853,0.022839,-0.003248,0.99973,-12.683 > view matrix models > #1,-0.94293,-0.29197,-0.16012,135,0.33274,-0.84487,-0.4189,79.3,-0.012978,-0.44828,0.8938,16.082 > view matrix models > #1,-0.98397,0.14482,-0.10409,115.23,-0.14104,-0.98908,-0.042846,80.216,-0.10915,-0.027479,0.99364,-3.6143 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.98397,0.14482,-0.10409,116.77,-0.14104,-0.98908,-0.042846,34.526,-0.10915,-0.027479,0.99364,-7.383 > view matrix models > #1,-0.98397,0.14482,-0.10409,129.19,-0.14104,-0.98908,-0.042846,34.931,-0.10915,-0.027479,0.99364,8.2471 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.65912,-0.68076,-0.31957,161.67,0.51961,-0.10506,-0.84792,30.444,0.54366,-0.72493,0.42297,47.06 > view matrix models > #1,-0.76831,0.43248,-0.47187,136.7,0.060618,0.78305,0.61899,-103.46,0.6372,0.44698,-0.62785,84.674 > view matrix models > #1,-0.98248,0.025355,-0.18463,140.71,-0.16057,0.38766,0.90771,-99.638,0.094587,0.92145,-0.3768,75.622 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.98248,0.025355,-0.18463,135.13,-0.16057,0.38766,0.90771,-59.244,0.094587,0.92145,-0.3768,70.638 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.99193,-0.062378,0.1104,114.02,0.080803,0.36003,0.92944,-73.872,-0.097723,0.93085,-0.35208,79.212 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.99193,-0.062378,0.1104,107.05,0.080803,0.36003,0.92944,-72.704,-0.097723,0.93085,-0.35208,82.111 > view matrix models > #1,-0.99193,-0.062378,0.1104,114.49,0.080803,0.36003,0.92944,-93.699,-0.097723,0.93085,-0.35208,57.904 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.9571,0.28849,0.027023,105.65,0.26877,0.84906,0.45481,-83.486,0.10827,0.44256,-0.89018,111.31 > view matrix models > #1,-0.94424,0.30785,-0.11683,116.4,0.29468,0.94837,0.11729,-60.158,0.1469,0.076325,-0.9862,131.83 > view matrix models > #1,-0.94238,0.31033,-0.12494,116.89,0.2985,0.94864,0.10481,-59.325,0.15105,0.061479,-0.98661,132.21 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.94238,0.31033,-0.12494,117.63,0.2985,0.94864,0.10481,-30.747,0.15105,0.061479,-0.98661,147.91 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.94444,0.32578,-0.043662,110.21,0.27276,0.85091,0.44895,-54.711,0.18341,0.4121,-0.89249,124.11 > view matrix models > #1,-0.94484,0.32551,-0.036316,109.62,0.27314,0.84426,0.46112,-55.505,0.18076,0.42576,-0.8866,123.21 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.94484,0.32551,-0.036316,107.15,0.27314,0.84426,0.46112,-64.24,0.18076,0.42576,-0.8866,119.63 > view matrix models > #1,-0.94484,0.32551,-0.036316,106.11,0.27314,0.84426,0.46112,-64.181,0.18076,0.42576,-0.8866,125.67 > ui tool show Match→Align > msa3d #1/A#2/A Match→Align cutoff: 5.0, in column if within cutoff of: any 24 residue pairs aligned 285 fully populated columns Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/tool.py"", line 199, in bbox.button(qbbox.Apply).clicked.connect(lambda *args, ma=self.match_align: ma(apply=True)) ^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/tool.py"", line 259, in match_align run(self.session, ""msa3d "" + ' '.join(args)) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 155, in make_alignment coords[seq] = column_atoms(seq, full_cols).scene_coords ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 247, in column_atoms return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 247, in return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'principal_atom' AttributeError: 'NoneType' object has no attribute 'principal_atom' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 247, in return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^ See log for complete Python traceback. > select #2/B 2350 atoms, 2405 bonds, 300 residues, 1 model selected > cartoon hide sel > select add #2 4164 atoms, 4276 bonds, 531 residues, 1 model selected > select add #1 9076 atoms, 8825 bonds, 6 pseudobonds, 1601 residues, 5 models selected > select subtract #2 4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected > view matrix models > #1,-0.94484,0.32551,-0.036316,78.784,0.27314,0.84426,0.46112,-98.282,0.18076,0.42576,-0.8866,101.33 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.89216,0.34963,-0.28601,96.076,0.30726,0.93384,0.18313,-80.114,0.33111,0.075506,-0.94057,111.2 > view matrix models > #1,-0.8876,-0.11044,-0.44717,127.82,0.45344,-0.38012,-0.80616,47.982,-0.080945,-0.91832,0.38747,61.2 > view matrix models > #1,-0.72558,-0.22625,-0.64988,140.38,0.61137,-0.64542,-0.45789,19.765,-0.31585,-0.72955,0.60662,48.529 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.72558,-0.22625,-0.64988,154.97,0.61137,-0.64542,-0.45789,58.622,-0.31585,-0.72955,0.60662,76.034 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.78266,-0.3287,-0.52858,151.99,0.44768,-0.88726,-0.11113,48.09,-0.43246,-0.32362,0.84158,46.59 > view matrix models > #1,-0.93745,-0.34808,0.0054046,116.15,0.33548,-0.90742,-0.25307,67.435,0.092993,-0.23543,0.96743,2.1588 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.93745,-0.34808,0.0054046,134.19,0.33548,-0.90742,-0.25307,62.876,0.092993,-0.23543,0.96743,7.7984 > view matrix models > #1,-0.93745,-0.34808,0.0054046,134.81,0.33548,-0.90742,-0.25307,63.104,0.092993,-0.23543,0.96743,6.9425 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.89951,-0.31276,0.30507,105.68,0.23313,-0.93413,-0.27028,71.515,0.36951,-0.172,0.91317,-6.847 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.89951,-0.31276,0.30507,101.6,0.23313,-0.93413,-0.27028,72.531,0.36951,-0.172,0.91317,-8.3189 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.89907,-0.3103,0.30885,101.15,0.23415,-0.93688,-0.25966,71.677,0.36993,-0.16114,0.91498,-8.9289 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.89907,-0.3103,0.30885,100.24,0.23415,-0.93688,-0.25966,77.531,0.36993,-0.16114,0.91498,-12.425 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.8404,-0.54186,-0.010584,133.29,0.39205,-0.59435,-0.70217,92.555,0.37419,-0.59426,0.71193,21.838 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.8404,-0.54186,-0.010584,128.48,0.39205,-0.59435,-0.70217,86.68,0.37419,-0.59426,0.71193,20.236 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.89687,-0.44211,-0.012456,127.92,0.31477,-0.61825,-0.7202,93.609,0.31071,-0.64985,0.69365,27.65 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.89687,-0.44211,-0.012456,127.52,0.31477,-0.61825,-0.7202,95.437,0.31071,-0.64985,0.69365,29.561 > view matrix models > #1,-0.89687,-0.44211,-0.012456,124.44,0.31477,-0.61825,-0.7202,92.625,0.31071,-0.64985,0.69365,32.887 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.65267,-0.75749,-0.015254,123.17,0.48571,-0.40288,-0.77574,78.977,0.58147,-0.51371,0.63087,17.266 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.65267,-0.75749,-0.015254,131.65,0.48571,-0.40288,-0.77574,74.387,0.58147,-0.51371,0.63087,17.936 > view matrix models > #1,-0.65267,-0.75749,-0.015254,132.85,0.48571,-0.40288,-0.77574,82.595,0.58147,-0.51371,0.63087,11.574 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.63655,-0.75476,0.15853,117,0.67528,-0.64475,-0.35817,45.724,0.37255,-0.12094,0.9201,-16.667 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.63655,-0.75476,0.15853,115.14,0.67528,-0.64475,-0.35817,39.093,0.37255,-0.12094,0.9201,-17.536 > ui tool show Match→Align > msa3d #2/A#1/A cutoffDistance 10 maxIterations none refChain #1/A Match→Align cutoff: 10.0, in column if within cutoff of: any 67 residue pairs aligned 285 fully populated columns 285 fully populated columns in at least 3 column stetches Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/tool.py"", line 259, in match_align run(self.session, ""msa3d "" + ' '.join(args)) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 129, in make_alignment ref_atoms = column_atoms(ref_seq, culled) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 247, in column_atoms return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 247, in return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'principal_atom' AttributeError: 'NoneType' object has no attribute 'principal_atom' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 247, in return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z1610005LLL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 10 days, 8 hours, 33 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.1.2 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 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: 1.67.1 ChimeraX-AtomicLibrary: 14.4 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: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3.1 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12.dev202604220250 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: 1.2.1 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: 1.8.2 ChimeraX-Label: 1.3 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 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-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.3 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.5.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 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: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.5 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.2 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.5 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.62.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.12 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 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: 6.7.1 narwhals: 2.20.0 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: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.6 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: 4.9.6 plotly: 6.7.0 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: 2.13.3 pydantic-settings: 2.14.0 pydantic_core: 2.46.3 pydata-sphinx-theme: 0.17.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.0 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: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.26 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 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: 9.0.4 sphinx-autodoc-typehints: 3.6.1 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: 3.3.4 stack-data: 0.6.3 starlette: 1.0.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.5 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.6.3 uvicorn: 0.45.0 wcwidth: 0.6.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.23.0 }}} " defect closed normal Sequence duplicate all ChimeraX