id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17304 pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib) clmarino@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.4-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Replace this text with list of actions that caused this problem to occur Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > set bgColor #01010100 > set bgColor #3b3b3b00 > set bgColor #6a6a6a00 > set bgColor #a7a7a700 > set bgColor #e6e6e600 > set bgColor #ffffff00 > set bgColor #fcfcfc00 > set bgColor #67676700 > set bgColor #10101000 > set bgColor transparent No atoms, bonds, or surfaces visible > open /Users/ghalib/Downloads/3maw.pdb 3maw.pdb title: Structure of the newcastle disease virus F protein In the post-fusion conformation [more info...] Chain information for 3maw.pdb #1 --- Chain | Description | UniProt A B | fusion glycoprotein F0 | FUS_NDVA 32-499 Non-standard residues in 3maw.pdb #1 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) NDG — 2-acetamido-2-deoxy-α-D-glucopyranose (N-acetyl-α-D-glucosamine; 2-acetamido-2-deoxy-α-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; 2-(acetylamino)-2-deoxy-A-D-glucopyranose) > set bgColor white > set bgColor #ffffff00 > color byhetero > color bychain > color bypolymer > rainbow > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A ARG 35 /A LYS 48 /A LYS 64 /A MET 69 /A LYS 73 /A ASN 145 /A GLN 146 /A ILE 151 /A ARG 153 /A THR 161 /A LYS 181 /A GLN 205 /A LYS 252 /A LEU 343 /A LYS 374 /A LEU 386 /A ARG 421 /A ILE 432 /A LEU 434 /A ILE 463 /A ASN 472 /A LEU 478 /A LYS 480 /A GLU 482 /A GLU 483 /A LYS 487 /A LYS 490 /A ASN 492 /A VAL 493 /B ARG 35 /B LYS 48 /B LYS 64 /B MET 69 /B LYS 73 /B ASN 145 /B GLN 146 /B ILE 151 /B ARG 153 /B THR 161 /B LYS 181 /B GLN 205 /B LYS 252 /B LEU 343 /B LYS 374 /B LEU 386 /B ARG 421 /B ILE 432 /B LEU 434 /B ILE 463 /B ASN 472 /B LEU 478 /B LYS 480 /B GLU 482 /B GLU 483 /B LYS 487 /B LYS 490 /B ASN 492 /B VAL 493 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 3maw.pdb_A SES surface #1.2: minimum, -17.65, mean -3.54, maximum 9.41 Coulombic values for 3maw.pdb_B SES surface #1.3: minimum, -17.48, mean -3.59, maximum 8.92 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for 3maw.pdb_A SES surface #1.2: minimum, -17.65, mean -3.54, maximum 9.41 Coulombic values for 3maw.pdb_B SES surface #1.3: minimum, -17.48, mean -3.59, maximum 8.92 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for 3maw.pdb_A SES surface #1.2: minimum, -17.65, mean -3.54, maximum 9.41 Coulombic values for 3maw.pdb_B SES surface #1.3: minimum, -17.48, mean -3.59, maximum 8.92 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""3maw.pdb_A SES surface"": minimum -30.16, mean -4.837, maximum 25.07 Map values for surface ""3maw.pdb_B SES surface"": minimum -29.73, mean -4.742, maximum 27.32 To also show corresponding color key, enter the above mlp command and add key true > color bfactor 6184 atoms, 846 residues, 2 surfaces, atom bfactor range 59.1 to 239 > hbonds reveal true 544 hydrogen bonds found > color bynucleotide [Repeated 1 time(s)] > color byhetero > color bypolymer > color bychain > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > style stick Changed 6184 atom styles > nucleotides fill > style nucleic stick Changed 0 atom styles > show atoms > hide atoms > hide cartoons > show cartoons > show surfaces > show atoms > hbonds reveal true 544 hydrogen bonds found > interfaces ~solvent 0 buried areas: > color byhetero > color bynucleotide > color byhetero > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > undo > hbonds reveal true 544 hydrogen bonds found > color bfactor 6184 atoms, 846 residues, 2 surfaces, atom bfactor range 59.1 to 239 > undo > rainbow > ~hbonds [Repeated 2 time(s)] > hbonds reveal true 544 hydrogen bonds found > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... Errors may have occurred when running pip: pip standard error: \--- ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.4 which is incompatible. nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= ""3.8"", but you have numpy 2.2.4 which is incompatible. \--- pip standard output: \--- \--- > kvfinder Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/tool.py"", line 67, in find_cavities run(self.session, ""kvfinder %s"" % concise_model_spec(self.session, structures, File ""/Applications/ChimeraX-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/cmd.py"", line 52, in cmd_kvfinder num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices, grid_spacing, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/pyKVFinder/grid.py"", line 820, in detect from _pyKVFinder import _detect, _detect_ladj ImportError: dlopen(/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried: '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)), '/System/Volumes/Preboot/Cryptexes/OS/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (no such file), '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) ImportError: dlopen(/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried: '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)), '/System/Volumes/Preboot/Cryptexes/OS/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (no such file), '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) File ""/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/pyKVFinder/grid.py"", line 820, in detect from _pyKVFinder import _detect, _detect_ladj See log for complete Python traceback. > ui tool show ""Find Cavities"" > kvfinder Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/tool.py"", line 67, in find_cavities run(self.session, ""kvfinder %s"" % concise_model_spec(self.session, structures, File ""/Applications/ChimeraX-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/cmd.py"", line 52, in cmd_kvfinder num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices, grid_spacing, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/pyKVFinder/grid.py"", line 820, in detect from _pyKVFinder import _detect, _detect_ladj ImportError: dlopen(/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried: '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)), '/System/Volumes/Preboot/Cryptexes/OS/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (no such file), '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) ImportError: dlopen(/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried: '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)), '/System/Volumes/Preboot/Cryptexes/OS/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (no such file), '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) File ""/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/pyKVFinder/grid.py"", line 820, in detect from _pyKVFinder import _detect, _detect_ladj See log for complete Python traceback. > kvfinder Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/cmd.py"", line 52, in cmd_kvfinder num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices, grid_spacing, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/pyKVFinder/grid.py"", line 820, in detect from _pyKVFinder import _detect, _detect_ladj ImportError: dlopen(/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried: '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)), '/System/Volumes/Preboot/Cryptexes/OS/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (no such file), '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) ImportError: dlopen(/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried: '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)), '/System/Volumes/Preboot/Cryptexes/OS/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (no such file), '/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) File ""/Users/ghalib/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/pyKVFinder/grid.py"", line 820, in detect from _pyKVFinder import _detect, _detect_ladj See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z15S00112HN/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4 (24E248) Kernel Version: Darwin 24.4.0 Time since boot: 2 days, 10 hours, 29 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 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: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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-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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 narwhals: 1.33.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 2.2.4 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 plotly: 6.0.1 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.7.3 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Surface/Binding Analysis fixed chimera-programmers ubaumann@… all ChimeraX