Changes between Initial Version and Version 3 of Ticket #9214


Ignore:
Timestamp:
Oct 19, 2023, 4:45:23 PM (2 years ago)
Author:
Greg Couch
Comment:

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  • Ticket #9214

    • Property Component Unassigned → Input/Output
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Milestone → 1.7

  • Ticket #9214 – Description

    initial v3  
    22Hi,
    33
    4 
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    8 
    9 
    104(Describe the actions that caused this problem to occur here)
    115
    126In 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?
    137
    14 
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    208save 0619_F&G_final_computedSheets.mmcif computedSheets true
    219
    22 
    23 
    24 
    2510Not saving entity_poly_seq for non-authoritative sequences
    26 
    2711old strand order: ('S1', 1) ('S2', 3)
    28 
    2912old strand order: ('S1', 3) ('S2', 3)
    30 
    3113old strand order: ('S1', 5) ('S2', 3)
    32 
    3314old strand order: ('S1', 5) ('S2', 4)
    34 
    3515old strand order: ('S2', 3) ('S1', 1)
    36 
    3716old strand order: ('S2', 3) ('S1', 3)
    38 
    3917old strand order: ('S2', 3) ('S1', 5)
    40 
    4118old strand order: ('S2', 4) ('S1', 5)
    42 
    4319old strand order: ('S3', 2) ('S242', 1)
    44 
    4520old strand order: ('S3', 1) ('S242', 2)
    46 
    4721Traceback (most recent call last):
    48 
    4922File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 319, in execute
    50 
    5123cmd.run(cmd_text)
    52 
    5324File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run
    54 
    5525result = ci.function(session, **kw_args)
    56 
    5726File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\save_command\cmd.py", line 75, in cmd_save
    58 
    5927Command(session, registry=registry).run(provider_cmd_text, log=log)
    60 
    6128File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run
    62 
    6329result = ci.function(session, **kw_args)
    64 
    6530File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\save_command\cmd.py", line 90, in provider_save
    66 
    6731saver_info.save(session, path, **provider_kw)
    68 
    6932File "D:\ChimeraX\ChimeraX1.6\bin\lib\site-packages\chimerax\mmcif\__init__.py", line 112, in save
    70 
    7133mmcif_write.write_mmcif(session, path, **kw)
    72 
    7334File "src\mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif
    74 
    7535File "src\mmcif_write.pyx", line 156, in chimerax.mmcif.mmcif_write.write_mmcif
    76 
    7736File "src\mmcif_write.pyx", line 892, in chimerax.mmcif.mmcif_write.save_structure
    78 
    7937File "src\mmcif_write.pyx", line 915, in chimerax.mmcif.mmcif_write.save_structure
    80 
    8138KeyError: 11
    82 
    83 
    84 
    85 
    8639KeyError: 11
    8740
    88 
    89 
    90 
    9141File "src\mmcif_write.pyx", line 915, in chimerax.mmcif.mmcif_write.save_structure
    9242
    9343
    94 
    95 
    9644OpenGL version: 3.3.0 NVIDIA 512.89
    97 
    9845OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
    99 
    10046OpenGL vendor: NVIDIA Corporation
    10147
    102 
    103 
    104 
    10548Python: 3.9.11
    106 
    10749Locale: zh_CN.cp936
    108 
    10950Qt version: PyQt6 6.4.2, Qt 6.4.2
    110 
    11151Qt runtime version: 6.4.3
    112 
    11352Qt platform: windows
    11453
    115 
    116 
    117 
    11854Manufacturer: MECHREVO
    119 
    12055Model: Z3 Air Series GM5TGEO
    121 
    12256OS: Microsoft Windows 11 家庭中文版 (Build 22621)
    123 
    12457Memory: 16,911,499,264
    125 
    12658MaxProcessMemory: 137,438,953,344
    127 
    12859CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
    129 
    13060OSLanguage: zh-CN
    13161
    132 
    133 
    134 
    13562Installed Packages:
    136 
    13763alabaster: 0.7.13
    138 
    13964appdirs: 1.4.4
    140 
    14165asttokens: 2.2.1
    142 
    14366Babel: 2.12.1
    144 
    14567backcall: 0.2.0
    146 
    14768beautifulsoup4: 4.11.2
    148 
    14969blockdiag: 3.0.0
    150 
    15170build: 0.10.0
    152 
    15371certifi: 2023.5.7
    154 
    15572cftime: 1.6.2
    156 
    15773charset-normalizer: 3.1.0
    158 
    15974ChimeraX-AddCharge: 1.5.9.1
    160 
    16175ChimeraX-AddH: 2.2.5
    162 
    16376ChimeraX-AlignmentAlgorithms: 2.0.1
    164 
    16577ChimeraX-AlignmentHdrs: 3.3.1
    166 
    16778ChimeraX-AlignmentMatrices: 2.1
    168 
    16979ChimeraX-Alignments: 2.9.3
    170 
    17180ChimeraX-AlphaFold: 1.0
    172 
    17381ChimeraX-AltlocExplorer: 1.0.3
    174 
    17582ChimeraX-AmberInfo: 1.0
    176 
    17783ChimeraX-Arrays: 1.1
    178 
    17984ChimeraX-Atomic: 1.43.10
    180 
    18185ChimeraX-AtomicLibrary: 10.0.6
    182 
    18386ChimeraX-AtomSearch: 2.0.1
    184 
    18587ChimeraX-AxesPlanes: 2.3.2
    186 
    18788ChimeraX-BasicActions: 1.1.2
    188 
    18989ChimeraX-BILD: 1.0
    190 
    19190ChimeraX-BlastProtein: 2.1.2
    192 
    19391ChimeraX-BondRot: 2.0.1
    194 
    19592ChimeraX-BugReporter: 1.0.1
    196 
    19793ChimeraX-BuildStructure: 2.8
    198 
    19994ChimeraX-Bumps: 1.0
    200 
    20195ChimeraX-BundleBuilder: 1.2.2
    202 
    20396ChimeraX-ButtonPanel: 1.0.1
    204 
    20597ChimeraX-CageBuilder: 1.0.1
    206 
    20798ChimeraX-CellPack: 1.0
    208 
    20999ChimeraX-Centroids: 1.3.2
    210 
    211100ChimeraX-ChangeChains: 1.0.2
    212 
    213101ChimeraX-CheckWaters: 1.3.1
    214 
    215102ChimeraX-ChemGroup: 2.0.1
    216 
    217103ChimeraX-Clashes: 2.2.4
    218 
    219104ChimeraX-ColorActions: 1.0.3
    220 
    221105ChimeraX-ColorGlobe: 1.0
    222 
    223106ChimeraX-ColorKey: 1.5.3
    224 
    225107ChimeraX-CommandLine: 1.2.5
    226 
    227108ChimeraX-ConnectStructure: 2.0.1
    228 
    229109ChimeraX-Contacts: 1.0.1
    230 
    231110ChimeraX-Core: 1.6.1
    232 
    233111ChimeraX-CoreFormats: 1.1
    234 
    235112ChimeraX-coulombic: 1.4.2
    236 
    237113ChimeraX-Crosslinks: 1.0
    238 
    239114ChimeraX-Crystal: 1.0
    240 
    241115ChimeraX-CrystalContacts: 1.0.1
    242 
    243116ChimeraX-DataFormats: 1.2.3
    244 
    245117ChimeraX-Dicom: 1.2
    246 
    247118ChimeraX-DistMonitor: 1.4
    248 
    249119ChimeraX-DockPrep: 1.1.1
    250 
    251120ChimeraX-Dssp: 2.0
    252 
    253121ChimeraX-EMDB-SFF: 1.0
    254 
    255122ChimeraX-ESMFold: 1.0
    256 
    257123ChimeraX-FileHistory: 1.0.1
    258 
    259124ChimeraX-FunctionKey: 1.0.1
    260 
    261125ChimeraX-Geometry: 1.3
    262 
    263126ChimeraX-gltf: 1.0
    264 
    265127ChimeraX-Graphics: 1.1.1
    266 
    267128ChimeraX-Hbonds: 2.4
    268 
    269129ChimeraX-Help: 1.2.1
    270 
    271130ChimeraX-HKCage: 1.3
    272 
    273131ChimeraX-IHM: 1.1
    274 
    275132ChimeraX-ImageFormats: 1.2
    276 
    277133ChimeraX-IMOD: 1.0
    278 
    279134ChimeraX-IO: 1.0.1
    280 
    281135ChimeraX-ItemsInspection: 1.0.1
    282 
    283136ChimeraX-Label: 1.1.7
    284 
    285137ChimeraX-ListInfo: 1.1.1
    286 
    287138ChimeraX-Log: 1.1.5
    288 
    289139ChimeraX-LookingGlass: 1.1
    290 
    291140ChimeraX-Maestro: 1.8.2
    292 
    293141ChimeraX-Map: 1.1.4
    294 
    295142ChimeraX-MapData: 2.0
    296 
    297143ChimeraX-MapEraser: 1.0.1
    298 
    299144ChimeraX-MapFilter: 2.0.1
    300 
    301145ChimeraX-MapFit: 2.0
    302 
    303146ChimeraX-MapSeries: 2.1.1
    304 
    305147ChimeraX-Markers: 1.0.1
    306 
    307148ChimeraX-Mask: 1.0.2
    308 
    309149ChimeraX-MatchMaker: 2.0.12
    310 
    311150ChimeraX-MDcrds: 2.6
    312 
    313151ChimeraX-MedicalToolbar: 1.0.2
    314 
    315152ChimeraX-Meeting: 1.0.1
    316 
    317153ChimeraX-MLP: 1.1.1
    318 
    319154ChimeraX-mmCIF: 2.12
    320 
    321155ChimeraX-MMTF: 2.2
    322 
    323156ChimeraX-Modeller: 1.5.9
    324 
    325157ChimeraX-ModelPanel: 1.3.7
    326 
    327158ChimeraX-ModelSeries: 1.0.1
    328 
    329159ChimeraX-Mol2: 2.0
    330 
    331160ChimeraX-Mole: 1.0
    332 
    333161ChimeraX-Morph: 1.0.2
    334 
    335162ChimeraX-MouseModes: 1.2
    336 
    337163ChimeraX-Movie: 1.0
    338 
    339164ChimeraX-Neuron: 1.0
    340 
    341165ChimeraX-Nifti: 1.0
    342 
    343166ChimeraX-NRRD: 1.0
    344 
    345167ChimeraX-Nucleotides: 2.0.3
    346 
    347168ChimeraX-OpenCommand: 1.10.1
    348 
    349169ChimeraX-PDB: 2.7.2
    350 
    351170ChimeraX-PDBBio: 1.0
    352 
    353171ChimeraX-PDBLibrary: 1.0.2
    354 
    355172ChimeraX-PDBMatrices: 1.0
    356 
    357173ChimeraX-PickBlobs: 1.0.1
    358 
    359174ChimeraX-Positions: 1.0
    360 
    361175ChimeraX-PresetMgr: 1.1
    362 
    363176ChimeraX-PubChem: 2.1
    364 
    365177ChimeraX-ReadPbonds: 1.0.1
    366 
    367178ChimeraX-Registration: 1.1.1
    368 
    369179ChimeraX-RemoteControl: 1.0
    370 
    371180ChimeraX-RenderByAttr: 1.1
    372 
    373181ChimeraX-RenumberResidues: 1.1
    374 
    375182ChimeraX-ResidueFit: 1.0.1
    376 
    377183ChimeraX-RestServer: 1.1
    378 
    379184ChimeraX-RNALayout: 1.0
    380 
    381185ChimeraX-RotamerLibMgr: 3.0
    382 
    383186ChimeraX-RotamerLibsDunbrack: 2.0
    384 
    385187ChimeraX-RotamerLibsDynameomics: 2.0
    386 
    387188ChimeraX-RotamerLibsRichardson: 2.0
    388 
    389189ChimeraX-SaveCommand: 1.5.1
    390 
    391190ChimeraX-SchemeMgr: 1.0
    392 
    393191ChimeraX-SDF: 2.0.1
    394 
    395192ChimeraX-Segger: 1.0
    396 
    397193ChimeraX-Segment: 1.0.1
    398 
    399194ChimeraX-SelInspector: 1.0
    400 
    401195ChimeraX-SeqView: 2.8.3
    402 
    403196ChimeraX-Shape: 1.0.1
    404 
    405197ChimeraX-Shell: 1.0.1
    406 
    407198ChimeraX-Shortcuts: 1.1.1
    408 
    409199ChimeraX-ShowSequences: 1.0.1
    410 
    411200ChimeraX-SideView: 1.0.1
    412 
    413201ChimeraX-Smiles: 2.1
    414 
    415202ChimeraX-SmoothLines: 1.0
    416 
    417203ChimeraX-SpaceNavigator: 1.0
    418 
    419204ChimeraX-StdCommands: 1.10.3
    420 
    421205ChimeraX-STL: 1.0.1
    422 
    423206ChimeraX-Storm: 1.0
    424 
    425207ChimeraX-StructMeasure: 1.1.2
    426 
    427208ChimeraX-Struts: 1.0.1
    428 
    429209ChimeraX-Surface: 1.0.1
    430 
    431210ChimeraX-SwapAA: 2.0.1
    432 
    433211ChimeraX-SwapRes: 2.2.1
    434 
    435212ChimeraX-TapeMeasure: 1.0
    436 
    437213ChimeraX-Test: 1.0
    438 
    439214ChimeraX-Toolbar: 1.1.2
    440 
    441215ChimeraX-ToolshedUtils: 1.2.1
    442 
    443216ChimeraX-Topography: 1.0
    444 
    445217ChimeraX-Tug: 1.0.1
    446 
    447218ChimeraX-UI: 1.28.4
    448 
    449219ChimeraX-uniprot: 2.2.2
    450 
    451220ChimeraX-UnitCell: 1.0.1
    452 
    453221ChimeraX-ViewDockX: 1.2
    454 
    455222ChimeraX-VIPERdb: 1.0
    456 
    457223ChimeraX-Vive: 1.1
    458 
    459224ChimeraX-VolumeMenu: 1.0.1
    460 
    461225ChimeraX-VTK: 1.0
    462 
    463226ChimeraX-WavefrontOBJ: 1.0
    464 
    465227ChimeraX-WebCam: 1.0.2
    466 
    467228ChimeraX-WebServices: 1.1.1
    468 
    469229ChimeraX-Zone: 1.0.1
    470 
    471230colorama: 0.4.6
    472 
    473231comm: 0.1.3
    474 
    475232comtypes: 1.1.14
    476 
    477233contourpy: 1.0.7
    478 
    479234cxservices: 1.2.2
    480 
    481235cycler: 0.11.0
    482 
    483236Cython: 0.29.33
    484 
    485237debugpy: 1.6.7
    486 
    487238decorator: 5.1.1
    488 
    489239docutils: 0.19
    490 
    491240executing: 1.2.0
    492 
    493241filelock: 3.9.0
    494 
    495242fonttools: 4.39.3
    496 
    497243funcparserlib: 1.0.1
    498 
    499244grako: 3.16.5
    500 
    501245h5py: 3.8.0
    502 
    503246html2text: 2020.1.16
    504 
    505247idna: 3.4
    506 
    507248ihm: 0.35
    508 
    509249imagecodecs: 2022.9.26
    510 
    511250imagesize: 1.4.1
    512 
    513251importlib-metadata: 6.6.0
    514 
    515252ipykernel: 6.21.1
    516 
    517253ipython: 8.10.0
    518 
    519254ipython-genutils: 0.2.0
    520 
    521255ipywidgets: 8.0.6
    522 
    523256jedi: 0.18.2
    524 
    525257Jinja2: 3.1.2
    526 
    527258jupyter-client: 8.0.2
    528 
    529259jupyter-core: 5.3.0
    530 
    531260jupyterlab-widgets: 3.0.7
    532 
    533261kiwisolver: 1.4.4
    534 
    535262line-profiler: 4.0.2
    536 
    537263lxml: 4.9.2
    538 
    539264lz4: 4.3.2
    540 
    541265MarkupSafe: 2.1.2
    542 
    543266matplotlib: 3.6.3
    544 
    545267matplotlib-inline: 0.1.6
    546 
    547268msgpack: 1.0.4
    548 
    549269nest-asyncio: 1.5.6
    550 
    551270netCDF4: 1.6.2
    552 
    553271networkx: 2.8.8
    554 
    555272nibabel: 5.0.1
    556 
    557273nptyping: 2.5.0
    558 
    559274numexpr: 2.8.4
    560 
    561275numpy: 1.23.5
    562 
    563276openvr: 1.23.701
    564 
    565277packaging: 23.1
    566 
    567278ParmEd: 3.4.3
    568 
    569279parso: 0.8.3
    570 
    571280pep517: 0.13.0
    572 
    573281pickleshare: 0.7.5
    574 
    575282Pillow: 9.3.0
    576 
    577283pip: 23.0
    578 
    579284pkginfo: 1.9.6
    580 
    581285platformdirs: 3.5.0
    582 
    583286prompt-toolkit: 3.0.38
    584 
    585287psutil: 5.9.4
    586 
    587288pure-eval: 0.2.2
    588 
    589289pycollada: 0.7.2
    590 
    591290pydicom: 2.3.0
    592 
    593291Pygments: 2.14.0
    594 
    595292pynrrd: 1.0.0
    596 
    597293PyOpenGL: 3.1.5
    598 
    599294PyOpenGL-accelerate: 3.1.5
    600 
    601295pyparsing: 3.0.9
    602 
    603296pyproject-hooks: 1.0.0
    604 
    605297PyQt6-commercial: 6.4.2
    606 
    607298PyQt6-Qt6: 6.4.3
    608 
    609299PyQt6-sip: 13.4.1
    610 
    611300PyQt6-WebEngine-commercial: 6.4.0
    612 
    613301PyQt6-WebEngine-Qt6: 6.4.3
    614 
    615302python-dateutil: 2.8.2
    616 
    617303pytz: 2023.3
    618 
    619304pywin32: 305
    620 
    621305pyzmq: 25.0.2
    622 
    623306qtconsole: 5.4.0
    624 
    625307QtPy: 2.3.1
    626 
    627308RandomWords: 0.4.0
    628 
    629309requests: 2.28.2
    630 
    631310scipy: 1.9.3
    632 
    633311setuptools: 67.4.0
    634 
    635312sfftk-rw: 0.7.3
    636 
    637313six: 1.16.0
    638 
    639314snowballstemmer: 2.2.0
    640 
    641315sortedcontainers: 2.4.0
    642 
    643316soupsieve: 2.4.1
    644 
    645317sphinx: 6.1.3
    646 
    647318sphinx-autodoc-typehints: 1.22
    648 
    649319sphinxcontrib-applehelp: 1.0.4
    650 
    651320sphinxcontrib-blockdiag: 3.0.0
    652 
    653321sphinxcontrib-devhelp: 1.0.2
    654 
    655322sphinxcontrib-htmlhelp: 2.0.1
    656 
    657323sphinxcontrib-jsmath: 1.0.1
    658 
    659324sphinxcontrib-qthelp: 1.0.3
    660 
    661325sphinxcontrib-serializinghtml: 1.1.5
    662 
    663326stack-data: 0.6.2
    664 
    665327tables: 3.7.0
    666 
    667328tcia-utils: 1.2.0
    668 
    669329tifffile: 2022.10.10
    670 
    671330tinyarray: 1.2.4
    672 
    673331tomli: 2.0.1
    674 
    675332tornado: 6.3.1
    676 
    677333traitlets: 5.9.0
    678 
    679334typing-extensions: 4.5.0
    680 
    681335tzdata: 2023.3
    682 
    683336urllib3: 1.26.15
    684 
    685337wcwidth: 0.2.6
    686 
    687338webcolors: 1.12
    688 
    689339wheel: 0.38.4
    690 
    691340wheel-filename: 1.4.1
    692 
    693341widgetsnbextension: 4.0.7
    694 
    695342WMI: 1.5.1
    696 
    697343zipp: 3.15.0
    698 
    699 
    700 
    701344}}}