ChimeraX 1.6.1 can not save as mmcif format while computedSheets is true

[huwl2022@…]

Hi,







(Describe the actions that caused this problem to occur here)

In the chimerax version 1.6.1 on the platform of Windows-10-10.0.22621,when I run the following command to save a 120-chains-virus pdb as mmcif format, it seems something wrong. BTW, why is it so slow to open a mmcif file in the Chimera? Is there something wrong in my file?







save 0619_F&G_final_computedSheets.mmcif computedSheets true




Not saving entity_poly_seq for non-authoritative sequences

old strand order: ('S1', 1) ('S2', 3)

old strand order: ('S1', 3) ('S2', 3)

old strand order: ('S1', 5) ('S2', 3)

old strand order: ('S1', 5) ('S2', 4)

old strand order: ('S2', 3) ('S1', 1)

old strand order: ('S2', 3) ('S1', 3)

old strand order: ('S2', 3) ('S1', 5)

old strand order: ('S2', 4) ('S1', 5)

old strand order: ('S3', 2) ('S242', 1)

old strand order: ('S3', 1) ('S242', 2)

Traceback (most recent call last):

File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 319, in execute

cmd.run(cmd_text)

File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run

result = ci.function(session, **kw_args)

File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\save_command\cmd.py", line 75, in cmd_save

Command(session, registry=registry).run(provider_cmd_text, log=log)

File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run

result = ci.function(session, **kw_args)

File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\save_command\cmd.py", line 90, in provider_save

saver_info.save(session, path, **provider_kw)

File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\mmcif\__init__.py", line 112, in save

mmcif_write.write_mmcif(session, path, **kw)

File "src\mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif

File "src\mmcif_write.pyx", line 156, in chimerax.mmcif.mmcif_write.write_mmcif

File "src\mmcif_write.pyx", line 892, in chimerax.mmcif.mmcif_write.save_structure

File "src\mmcif_write.pyx", line 915, in chimerax.mmcif.mmcif_write.save_structure

KeyError: 11




KeyError: 11




File "src\mmcif_write.pyx", line 915, in chimerax.mmcif.mmcif_write.save_structure




OpenGL version: 3.3.0 NVIDIA 512.89

OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2

OpenGL vendor: NVIDIA Corporation




Python: 3.9.11

Locale: zh_CN.cp936

Qt version: PyQt6 6.4.2, Qt 6.4.2

Qt runtime version: 6.4.3

Qt platform: windows




Manufacturer: MECHREVO

Model: Z3 Air Series GM5TGEO

OS: Microsoft Windows 11 家庭中文版 (Build 22621)

Memory: 16,911,499,264

MaxProcessMemory: 137,438,953,344

CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz

OSLanguage: zh-CN




Installed Packages:

alabaster: 0.7.13

appdirs: 1.4.4

asttokens: 2.2.1

Babel: 2.12.1

backcall: 0.2.0

beautifulsoup4: 4.11.2

blockdiag: 3.0.0

build: 0.10.0

certifi: 2023.5.7

cftime: 1.6.2

charset-normalizer: 3.1.0

ChimeraX-AddCharge: 1.5.9.1

ChimeraX-AddH: 2.2.5

ChimeraX-AlignmentAlgorithms: 2.0.1

ChimeraX-AlignmentHdrs: 3.3.1

ChimeraX-AlignmentMatrices: 2.1

ChimeraX-Alignments: 2.9.3

ChimeraX-AlphaFold: 1.0

ChimeraX-AltlocExplorer: 1.0.3

ChimeraX-AmberInfo: 1.0

ChimeraX-Arrays: 1.1

ChimeraX-Atomic: 1.43.10

ChimeraX-AtomicLibrary: 10.0.6

ChimeraX-AtomSearch: 2.0.1

ChimeraX-AxesPlanes: 2.3.2

ChimeraX-BasicActions: 1.1.2

ChimeraX-BILD: 1.0

ChimeraX-BlastProtein: 2.1.2

ChimeraX-BondRot: 2.0.1

ChimeraX-BugReporter: 1.0.1

ChimeraX-BuildStructure: 2.8

ChimeraX-Bumps: 1.0

ChimeraX-BundleBuilder: 1.2.2

ChimeraX-ButtonPanel: 1.0.1

ChimeraX-CageBuilder: 1.0.1

ChimeraX-CellPack: 1.0

ChimeraX-Centroids: 1.3.2

ChimeraX-ChangeChains: 1.0.2

ChimeraX-CheckWaters: 1.3.1

ChimeraX-ChemGroup: 2.0.1

ChimeraX-Clashes: 2.2.4

ChimeraX-ColorActions: 1.0.3

ChimeraX-ColorGlobe: 1.0

ChimeraX-ColorKey: 1.5.3

ChimeraX-CommandLine: 1.2.5

ChimeraX-ConnectStructure: 2.0.1

ChimeraX-Contacts: 1.0.1

ChimeraX-Core: 1.6.1

ChimeraX-CoreFormats: 1.1

ChimeraX-coulombic: 1.4.2

ChimeraX-Crosslinks: 1.0

ChimeraX-Crystal: 1.0

ChimeraX-CrystalContacts: 1.0.1

ChimeraX-DataFormats: 1.2.3

ChimeraX-Dicom: 1.2

ChimeraX-DistMonitor: 1.4

ChimeraX-DockPrep: 1.1.1

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: 1.1.1

ChimeraX-Hbonds: 2.4

ChimeraX-Help: 1.2.1

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-Label: 1.1.7

ChimeraX-ListInfo: 1.1.1

ChimeraX-Log: 1.1.5

ChimeraX-LookingGlass: 1.1

ChimeraX-Maestro: 1.8.2

ChimeraX-Map: 1.1.4

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: 2.0.12

ChimeraX-MDcrds: 2.6

ChimeraX-MedicalToolbar: 1.0.2

ChimeraX-Meeting: 1.0.1

ChimeraX-MLP: 1.1.1

ChimeraX-mmCIF: 2.12

ChimeraX-MMTF: 2.2

ChimeraX-Modeller: 1.5.9

ChimeraX-ModelPanel: 1.3.7

ChimeraX-ModelSeries: 1.0.1

ChimeraX-Mol2: 2.0

ChimeraX-Mole: 1.0

ChimeraX-Morph: 1.0.2

ChimeraX-MouseModes: 1.2

ChimeraX-Movie: 1.0

ChimeraX-Neuron: 1.0

ChimeraX-Nifti: 1.0

ChimeraX-NRRD: 1.0

ChimeraX-Nucleotides: 2.0.3

ChimeraX-OpenCommand: 1.10.1

ChimeraX-PDB: 2.7.2

ChimeraX-PDBBio: 1.0

ChimeraX-PDBLibrary: 1.0.2

ChimeraX-PDBMatrices: 1.0

ChimeraX-PickBlobs: 1.0.1

ChimeraX-Positions: 1.0

ChimeraX-PresetMgr: 1.1

ChimeraX-PubChem: 2.1

ChimeraX-ReadPbonds: 1.0.1

ChimeraX-Registration: 1.1.1

ChimeraX-RemoteControl: 1.0

ChimeraX-RenderByAttr: 1.1

ChimeraX-RenumberResidues: 1.1

ChimeraX-ResidueFit: 1.0.1

ChimeraX-RestServer: 1.1

ChimeraX-RNALayout: 1.0

ChimeraX-RotamerLibMgr: 3.0

ChimeraX-RotamerLibsDunbrack: 2.0

ChimeraX-RotamerLibsDynameomics: 2.0

ChimeraX-RotamerLibsRichardson: 2.0

ChimeraX-SaveCommand: 1.5.1

ChimeraX-SchemeMgr: 1.0

ChimeraX-SDF: 2.0.1

ChimeraX-Segger: 1.0

ChimeraX-Segment: 1.0.1

ChimeraX-SelInspector: 1.0

ChimeraX-SeqView: 2.8.3

ChimeraX-Shape: 1.0.1

ChimeraX-Shell: 1.0.1

ChimeraX-Shortcuts: 1.1.1

ChimeraX-ShowSequences: 1.0.1

ChimeraX-SideView: 1.0.1

ChimeraX-Smiles: 2.1

ChimeraX-SmoothLines: 1.0

ChimeraX-SpaceNavigator: 1.0

ChimeraX-StdCommands: 1.10.3

ChimeraX-STL: 1.0.1

ChimeraX-Storm: 1.0

ChimeraX-StructMeasure: 1.1.2

ChimeraX-Struts: 1.0.1

ChimeraX-Surface: 1.0.1

ChimeraX-SwapAA: 2.0.1

ChimeraX-SwapRes: 2.2.1

ChimeraX-TapeMeasure: 1.0

ChimeraX-Test: 1.0

ChimeraX-Toolbar: 1.1.2

ChimeraX-ToolshedUtils: 1.2.1

ChimeraX-Topography: 1.0

ChimeraX-Tug: 1.0.1

ChimeraX-UI: 1.28.4

ChimeraX-uniprot: 2.2.2

ChimeraX-UnitCell: 1.0.1

ChimeraX-ViewDockX: 1.2

ChimeraX-VIPERdb: 1.0

ChimeraX-Vive: 1.1

ChimeraX-VolumeMenu: 1.0.1

ChimeraX-VTK: 1.0

ChimeraX-WavefrontOBJ: 1.0

ChimeraX-WebCam: 1.0.2

ChimeraX-WebServices: 1.1.1

ChimeraX-Zone: 1.0.1

colorama: 0.4.6

comm: 0.1.3

comtypes: 1.1.14

contourpy: 1.0.7

cxservices: 1.2.2

cycler: 0.11.0

Cython: 0.29.33

debugpy: 1.6.7

decorator: 5.1.1

docutils: 0.19

executing: 1.2.0

filelock: 3.9.0

fonttools: 4.39.3

funcparserlib: 1.0.1

grako: 3.16.5

h5py: 3.8.0

html2text: 2020.1.16

idna: 3.4

ihm: 0.35

imagecodecs: 2022.9.26

imagesize: 1.4.1

importlib-metadata: 6.6.0

ipykernel: 6.21.1

ipython: 8.10.0

ipython-genutils: 0.2.0

ipywidgets: 8.0.6

jedi: 0.18.2

Jinja2: 3.1.2

jupyter-client: 8.0.2

jupyter-core: 5.3.0

jupyterlab-widgets: 3.0.7

kiwisolver: 1.4.4

line-profiler: 4.0.2

lxml: 4.9.2

lz4: 4.3.2

MarkupSafe: 2.1.2

matplotlib: 3.6.3

matplotlib-inline: 0.1.6

msgpack: 1.0.4

nest-asyncio: 1.5.6

netCDF4: 1.6.2

networkx: 2.8.8

nibabel: 5.0.1

nptyping: 2.5.0

numexpr: 2.8.4

numpy: 1.23.5

openvr: 1.23.701

packaging: 23.1

ParmEd: 3.4.3

parso: 0.8.3

pep517: 0.13.0

pickleshare: 0.7.5

Pillow: 9.3.0

pip: 23.0

pkginfo: 1.9.6

platformdirs: 3.5.0

prompt-toolkit: 3.0.38

psutil: 5.9.4

pure-eval: 0.2.2

pycollada: 0.7.2

pydicom: 2.3.0

Pygments: 2.14.0

pynrrd: 1.0.0

PyOpenGL: 3.1.5

PyOpenGL-accelerate: 3.1.5

pyparsing: 3.0.9

pyproject-hooks: 1.0.0

PyQt6-commercial: 6.4.2

PyQt6-Qt6: 6.4.3

PyQt6-sip: 13.4.1

PyQt6-WebEngine-commercial: 6.4.0

PyQt6-WebEngine-Qt6: 6.4.3

python-dateutil: 2.8.2

pytz: 2023.3

pywin32: 305

pyzmq: 25.0.2

qtconsole: 5.4.0

QtPy: 2.3.1

RandomWords: 0.4.0

requests: 2.28.2

scipy: 1.9.3

setuptools: 67.4.0

sfftk-rw: 0.7.3

six: 1.16.0

snowballstemmer: 2.2.0

sortedcontainers: 2.4.0

soupsieve: 2.4.1

sphinx: 6.1.3

sphinx-autodoc-typehints: 1.22

sphinxcontrib-applehelp: 1.0.4

sphinxcontrib-blockdiag: 3.0.0

sphinxcontrib-devhelp: 1.0.2

sphinxcontrib-htmlhelp: 2.0.1

sphinxcontrib-jsmath: 1.0.1

sphinxcontrib-qthelp: 1.0.3

sphinxcontrib-serializinghtml: 1.1.5

stack-data: 0.6.2

tables: 3.7.0

tcia-utils: 1.2.0

tifffile: 2022.10.10

tinyarray: 1.2.4

tomli: 2.0.1

tornado: 6.3.1

traitlets: 5.9.0

typing-extensions: 4.5.0

tzdata: 2023.3

urllib3: 1.26.15

wcwidth: 0.2.6

webcolors: 1.12

wheel: 0.38.4

wheel-filename: 1.4.1

widgetsnbextension: 4.0.7

WMI: 1.5.1

zipp: 3.15.0