Opened 15 months ago
Closed 15 months ago
#15747 closed defect (fixed)
Morphing from an existing morph: IndexError
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Editing | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Simpler test case of bug #15743. Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7sti Summary of feedback from opening 7sti fetched from pdb --- note | Fetching compressed mmCIF 7sti from http://files.rcsb.org/download/7sti.cif 7sti title: Full-length insulin receptor bound with unsaturated insulin WT (1 insulin bound) asymmetric conformation [more info...] Chain information for 7sti #1 --- Chain | Description | UniProt A B | Insulin receptor | INSR_MOUSE -26-1343 C | Insulin | INS_HUMAN -23-76 > open 7stj Summary of feedback from opening 7stj fetched from pdb --- note | Fetching compressed mmCIF 7stj from http://files.rcsb.org/download/7stj.cif 7stj title: Full-length insulin receptor bound with unsaturated insulin WT (2 insulins bound) asymmetric conformation (Conformation 1) [more info...] Chain information for 7stj #2 --- Chain | Description | UniProt A B | Insulin receptor | INSR_MOUSE -26-1343 C D | Insulin | INS_HUMAN -23-76 > open 7sth 7sth title: Full-length insulin receptor bound with unsaturated insulin WT (2 insulin bound) symmetric conformation [more info...] Chain information for 7sth #3 --- Chain | Description | UniProt A B | Insulin receptor | INSR_MOUSE -26-1344 C D | Insulin | INS_HUMAN -23-76 > delete /C,D > morph #1,2 Computed 51 frame morph #4 > coordset #4 1,51 > morph #4,3 Traceback (most recent call last): File "/Users/goddard/Desktop/ChimeraX-1.8.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 "/Users/goddard/Desktop/ChimeraX-1.8.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 "/Users/goddard/Desktop/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/morph.py", line 84, in morph traj = compute_morph(structures, session.logger, method=method, rate=rate, frames=frames, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py", line 28, in compute_morph motion.interpolate(res_groups, atom_map, res_interp) File "/Users/goddard/Desktop/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ IndexError: index 12776 is out of bounds for axis 0 with size 12776 IndexError: index 12776 is out of bounds for axis 0 with size 12776 File "/Users/goddard/Desktop/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 Ultra OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 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: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 51 days, 23 hours, 4 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: aiobotocore: 2.12.3 aiohttp: 3.9.5 aioitertools: 0.11.0 aiosignal: 1.3.1 alabaster: 0.7.16 alphashape: 1.3.1 annotated-types: 0.6.0 appdirs: 1.4.4 appnope: 0.1.4 asciitree: 0.3.3 asttokens: 2.4.1 attrs: 23.2.0 Babel: 2.15.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 2.0.0 botocore: 1.34.69 build: 1.2.1 certifi: 2023.11.17 cffi: 1.16.0 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.4.7 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 ChimeraX-Clipper: 0.23.0 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-crai: 0.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-DeepSSETracer: 1.1 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NIHPresets: 1.1.17 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OME-Zarr: 0.5.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.2 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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-TetraScapeCommand: 0.1 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 click: 8.1.7 click-log: 0.4.0 cloudpickle: 3.0.0 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 copick: 0.1.dev45+g5a19260 cripser: 0.0.13 cryptography: 42.0.5 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 dask: 2024.4.2 debugpy: 1.8.1 decorator: 5.1.1 distributed: 2024.4.2 docutils: 0.20.1 executing: 2.0.1 fasteners: 0.19 filelock: 3.13.4 fonttools: 4.53.0 frozenlist: 1.4.1 fsspec: 2024.3.1 funcparserlib: 2.0.0a0 geomdl: 5.3.1 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 hatchling: 1.24.2 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imageio: 2.34.1 imagesize: 1.4.1 importlib-metadata: 4.0.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jmespath: 1.0.1 joblib: 1.4.0 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 lazy-loader: 0.4 line-profiler: 4.1.2 llvmlite: 0.42.0 locket: 1.0.0 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.0 msgpack: 1.0.8 multidict: 6.0.5 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numba: 0.59.1 numcodecs: 0.12.1 numexpr: 2.10.0 numpy: 1.26.4 ome-zarr: 0.8.3 openvr: 1.26.701 packaging: 23.2 pandas: 2.2.2 ParmEd: 4.2.2 parso: 0.8.4 partd: 1.4.1 pathspec: 0.12.1 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 pluggy: 1.5.0 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pyarrow: 16.0.0 pycollada: 0.8 pycparser: 2.22 pydantic: 2.7.1 pydantic-core: 2.18.2 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynndescent: 0.5.12 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 pyspnego: 0.10.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 PyYAML: 6.0.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 Rtree: 1.1.0 s3fs: 2024.3.1 scikit-image: 0.23.2 scikit-learn: 1.4.2 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 shapely: 2.0.2 six: 1.16.0 smbprotocol: 1.13.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 starfile: 0.5.6 superqt: 0.6.3 sympy: 1.12 tables: 3.8.0 tblib: 3.0.0 tcia-utils: 1.5.1 threadpoolctl: 3.4.0 tifffile: 2024.1.30 tinyarray: 1.2.4 toolz: 0.12.1 torch: 2.1.2 tornado: 6.4.1 tqdm: 4.66.2 traitlets: 5.14.2 trimesh: 4.0.10 trove-classifiers: 2024.4.10 typing-extensions: 4.12.2 tzdata: 2024.1 umap-learn: 0.5.6 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 wrapt: 1.16.0 yarl: 1.9.4 zarr: 2.17.2 zict: 3.0.0 zipp: 3.18.1
Change History (4)
comment:1 by , 15 months ago
Component: | Unassigned → Structure Editing |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Morphing from an existing morph: IndexError |
comment:2 by , 15 months ago
Get a different traceback in ChimeraX 1.9 development build
morph #4,3Traceback (most recent call last): File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/motion.py", line 111, in segment_and_pair_atoms results = segmentHingeExact(sm, m, cf, mhs, log=log) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/segment.py", line 109, in segmentHingeExact raise AtomPairingError('%s chain %s (%d) and %s chain %s (%d) have different number of residues' chimerax.morph.segment.AtomPairingError: Morph - Morph - 7sti chain A (786) and 7sth chain A (820) have different number of residues During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/goddard/ucsf/chimerax/ChimeraX.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 "/Users/goddard/ucsf/chimerax/ChimeraX.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 "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/morph.py", line 84, in morph traj = compute_morph(structures, session.logger, method=method, rate=rate, frames=frames, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/motion.py", line 24, in compute_morph res_groups, atom_map, trimmed = motion.segment_and_pair_atoms(mol) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/motion.py", line 114, in segment_and_pair_atoms results = segmentHingeApproximate(sm, m, cf, mhs, log=log) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/segment.py", line 223, in segmentHingeApproximate segments = find_hinges(parts, fraction, min_hinge_spacing, log) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/segment.py", line 302, in find_hinges segs = segmentHingeResidues(rList0, rList1, fraction, min_hinge_spacing) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/segment.py", line 310, in segmentHingeResidues segments = segmentSieve(rList0, rList1, fraction) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/segment.py", line 23, in segmentSieve coreList0, coreList1 = sieve_fit.fitResidues(rList0, rList1, fraction) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/sieve_fit.py", line 28, in fitResidues if not sieve(aList0, aList1, maxrmsd): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/sieve_fit.py", line 40, in sieve p, rms = align_points(position1, position0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/align.py", line 62, in align_points evals, evecs = linalg.eig(P) # eigenvectors are columns ^^^^^^^^^^^^^ File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/linalg/linalg.py", line 1329, in eig _assert_finite(a) File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/linalg/linalg.py", line 218, in _assert_finite raise LinAlgError("Array must not contain infs or NaNs") numpy.linalg.LinAlgError: Array must not contain infs or NaNs numpy.linalg.LinAlgError: Array must not contain infs or NaNs File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/linalg/linalg.py", line 218, in _assert_finite raise LinAlgError("Array must not contain infs or NaNs") See log for complete Python traceback.
comment:3 by , 15 months ago
The code appears to copy just the single active coordinate set for the first model in morph #4,3 which is the #4 coordinate set. But somehow that wipes out. Since model #4 is just a morph from #1 to #2 currently showing the coordinates of #2 it should be essentially the same as #2 (I say essentially since maybe altlocs are deleted in the coordinate sets version). If I try morph #2,3 it works.
Needs a more investigation. I guess it is some weirdness about coordinate sets causing the problem.
comment:4 by , 15 months ago
Resolution: | → fixed |
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Status: | assigned → closed |
Fixed.
The morph code copied the first model and since it had multiple coordinate sets it deleted all its coordinate sets and added back just the active coordinate set. But when it added it back it just used atoms.coords. Due to atom deletions the coordinates array was larger than the number of atoms and atoms.coord_indices had gaps. The copying code needed to allocate the original size array with the gaps because the atoms.coord_indices don't get updated. So I made it use the original coord_indices.
Simpler test case of bug #15743.