Restore session: invalid MRC header value

[andysen@…]

The following bug report has been submitted:
Platform:        macOS-14.3-arm64-arm-64bit
ChimeraX Version: 1.8rc202406102315 (2024-06-10 23:15:52 UTC)
Description
cannot open the session

Log:
UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Volumes/Extreme Pro/P1/tail/sheath_normal/new/session_fit_whole.cxs"

Error opening map "/Volumes/Extreme
Pro/P1/tail/sheath_normal/new/session_fit_whole.cxs": File
session_fit_whole.cxs, format mrc  
MRC header value nsymbt (15866409) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 757, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Wed May 10 14:32:25 2023UCSF ChimeraX version: 1.5.dev202210110346
(2022-10-11)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Volumes/Anindito/P1/tail/sheath_normal/new/session_fit_1.cxs format
> session

Unable to parse symmetry operators of P1_tail.mrc  
b'{\n\t"compression": 0, \n\t"filename": "P1_tail.mrc", \n\t"image":
[{\n\t\t"average": 0.00149451, \n\t\t"background": 0, \n\t\t"fom": 1,
\n\t\t"maximum": 0.501089, \n\t\t"minimum": -0.293842, \n\t\t"number": 1,
\n\t\t"origin": [\n\t\t\t256, 256, 256\n\t\t], \n\t\t"sampling":
[\n\t\t\t0.69445, 0.69445, 0.69445\n\t\t], \n\t\t"select": 1,
\n\t\t"standard_deviation": 0.031601, \n\t\t"view": [\n\t\t\t0, 0, 1,
0\n\t\t]\n\t}], \n\t"label": "bimg -verb 7 -size 512,512,512 -origin
256,256,256 -samp 0.69445 cryosparc_P4_J176_006_volume_map_sharp.mrc
P1_tail.mrc ", \n\t"pointgroup": "C1", \n\t"spacegroup": 0, \n\t"time":
1658610729, \n\t"user": "andy", \n\t"version": "2.1.3-20210901"\n}\n'  
  
Opened P1_tail.mrc as #1, grid size 512,512,512, pixel 0.694,0.694,0.694,
shown at level 0.1, step 1, values float32  
Log from Wed May 10 12:57:24 2023UCSF ChimeraX version: 1.5.dev202210110346
(2022-10-11)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Volumes/Anindito/P1/tail/sheath_normal/all_previous/ses1.cxs format
> session

Unable to parse symmetry operators of P1_tail.mrc  
b'{\n\t"compression": 0, \n\t"filename": "P1_tail.mrc", \n\t"image":
[{\n\t\t"average": 0.00149451, \n\t\t"background": 0, \n\t\t"fom": 1,
\n\t\t"maximum": 0.501089, \n\t\t"minimum": -0.293842, \n\t\t"number": 1,
\n\t\t"origin": [\n\t\t\t256, 256, 256\n\t\t], \n\t\t"sampling":
[\n\t\t\t0.69445, 0.69445, 0.69445\n\t\t], \n\t\t"select": 1,
\n\t\t"standard_deviation": 0.031601, \n\t\t"view": [\n\t\t\t0, 0, 1,
0\n\t\t]\n\t}], \n\t"label": "bimg -verb 7 -size 512,512,512 -origin
256,256,256 -samp 0.69445 cryosparc_P4_J176_006_volume_map_sharp.mrc
P1_tail.mrc ", \n\t"pointgroup": "C1", \n\t"spacegroup": 0, \n\t"time":
1658610729, \n\t"user": "andy", \n\t"version": "2.1.3-20210901"\n}\n'  
  
Opened P1_tail.mrc as #1, grid size 512,512,512, pixel 0.694,0.694,0.694,
shown at level 0.1, step 1, values float32  
Log from Sat Jul 23 16:26:39 2022UCSF ChimeraX version: 1.3.dev202104230049
(2021-04-23)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/andy/Documents/p1/sheath_normal/P1_tail.mrc

Summary of feedback from opening
/Users/andy/Documents/p1/sheath_normal/P1_tail.mrc  
---  
notes | Unable to parse symmetry operators of P1_tail.mrc  
b'{\n\t"compression": 0, \n\t"filename": "P1_tail.mrc", \n\t"image":
[{\n\t\t"average": 0.00149451, \n\t\t"background": 0, \n\t\t"fom": 1,
\n\t\t"maximum": 0.501089, \n\t\t"minimum": -0.293842, \n\t\t"number": 1,
\n\t\t"origin": [\n\t\t\t256, 256, 256\n\t\t], \n\t\t"sampling":
[\n\t\t\t0.69445, 0.69445, 0.69445\n\t\t], \n\t\t"select": 1,
\n\t\t"standard_deviation": 0.031601, \n\t\t"view": [\n\t\t\t0, 0, 1,
0\n\t\t]\n\t}], \n\t"label": "bimg -verb 7 -size 512,512,512 -origin
256,256,256 -samp 0.69445 cryosparc_P4_J176_006_volume_map_sharp.mrc
P1_tail.mrc ", \n\t"pointgroup": "C1", \n\t"spacegroup": 0, \n\t"time":
1658610729, \n\t"user": "andy", \n\t"version": "2.1.3-20210901"\n}\n'  
  
Opened P1_tail.mrc as #1, grid size 512,512,512, pixel 0.694,0.694,0.694,
shown at level 0.152, step 2, values float32  

> volume #1 step 1

> lighting soft

> volume #1 level 0.1

> lighting shadows true intensity 0.5

> lighting full

> ui tool show "Side View"

> ui tool show "Surface Color"

> color cylindrical #1.1 palette #ff0000:#ffffff:#0000ff center
> -7.6294e-06,0,1.043

> ac wb

Unknown command: ac wb  

> set bgColor white

> color cylindrical #1.1 palette 0,#ff0000:80,#ffffff:100.4,#0000ff center
> -7.6294e-06,0,1.043

> color cylindrical #1.1 palette 0,#ff0000:80,#ffffff:90,#0000ff center
> -7.6294e-06,0,1.043

> color cylindrical #1.1 palette 0,#ff0000:80,#ffffff:100,#0000ff center
> -7.6294e-06,0,1.043

> color cylindrical #1.1 palette 0,#ff0000:70,#ffffff:100,#0000ff center
> -7.6294e-06,0,1.043

> lighting soft

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting full

> graphics silhouettes true

> save /Users/andy/Documents/p1/sheath_normal/image2.tif width 740 height 597
> supersample 3

> color cylindrical #1.1 palette 0,#0000ff:70,#ffffff:100,#ff0000 center
> -7.6294e-06,0,1.043

> color cylindrical #1.1 palette 0,#ff0000:70,#ffffff:100,#0000ff center
> -7.6294e-06,0,1.043

> save /Users/andy/Documents/p1/sheath_normal/ses1.cxs

——— End of log from Sat Jul 23 16:26:39 2022 ———

opened ChimeraX session  

> open /Volumes/Anindito/P1/tail/sheath_normal/new/new_sheath_ring.pdb

Chain information for new_sheath_ring.pdb #2  
---  
Chain | Description  
B V W X Y Z | No description available  
  

> ui tool show "Side View"

> hide #!1 models

> select add #2

24018 atoms, 24504 bonds, 3174 residues, 1 model selected  

> show #!1 models

> select subtract #2

Nothing selected  

> select add #2

24018 atoms, 24504 bonds, 3174 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #2

24018 atoms, 24504 bonds, 3174 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #2

24018 atoms, 24504 bonds, 3174 residues, 1 model selected  

> ui mousemode right translate

> select clear

> show cartoons

> hide atoms

> volume #1 style mesh

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule new_sheath_ring.pdb (#2) to map P1_tail.mrc (#1) using 24018
atoms  
average map value = 0.03914, steps = 88  
shifted from previous position = 2.71  
rotated from previous position = 0.788 degrees  
atoms outside contour = 18944, contour level = 0.1  
  
Position of new_sheath_ring.pdb (#2) relative to P1_tail.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998631 -0.00406135 0.00329806 -0.61103413  
0.00410299 0.99991072 -0.01271664 2.36806838  
-0.00324612 0.01273000 0.99991370 -0.35889780  
Axis 0.92486505 0.23785035 0.29673533  
Axis point 0.00000000 26.94170884 188.05601229  
Rotation angle (degrees) 0.78823974  
Shift along axis -0.10837587  
  

> select add #2

24018 atoms, 24504 bonds, 3174 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> select subtract #2

Nothing selected  

> fitmap #2 inMap #1

Fit molecule new_sheath_ring.pdb (#2) to map P1_tail.mrc (#1) using 24018
atoms  
average map value = 0.1406, steps = 60  
shifted from previous position = 1.57  
rotated from previous position = 1.64 degrees  
atoms outside contour = 8243, contour level = 0.1  
  
Position of new_sheath_ring.pdb (#2) relative to P1_tail.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99979130 0.02040689 -0.00096007 -1.93526745  
-0.02040535 0.99979052 0.00159357 3.50327467  
0.00099238 -0.00157365 0.99999827 -0.74075150  
Axis -0.07728427 -0.04764227 -0.99587015  
Axis point 172.40236343 93.86907961 0.00000000  
Rotation angle (degrees) 1.17411536  
Shift along axis 0.72035408  
  

> cd /Volumes/Anindito/P1/tail/sheath_normal/new

Current working directory is: /Volumes/Anindito/P1/tail/sheath_normal/new  

> save /Volumes/Anindito/P1/tail/sheath_normal/new/session_fit_1.cxs

——— End of log from Wed May 10 12:57:24 2023 ———

opened ChimeraX session  

> hide #!1 models

> show #!1 models

> select /B

4003 atoms, 4084 bonds, 529 residues, 1 model selected  

> select ~sel

20015 atoms, 20420 bonds, 2645 residues, 3 models selected  

> delete atoms (#2 & sel)

> delete bonds (#2 & sel)

> select clear

> sym #2 c6*h,39.15,19.32,6,-2

> save /Volumes/Anindito/P1/tail/sheath_normal/new/session_fit_whole.cxs

> lighting full

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting flat

> lighting full

> lighting soft

> lighting simple

> select : 401-529

992 atoms, 1012 bonds, 129 residues, 1 model selected  

> ui tool show "Color Actions"

> hide #!1 models

> show #!1 models

> select : 401-529

992 atoms, 1012 bonds, 129 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel fire brick

> select : 222-400

1347 atoms, 1375 bonds, 179 residues, 1 model selected  

> color sel cornflower blue

> select : 102-221

918 atoms, 933 bonds, 120 residues, 1 model selected  

> color sel salmon

> select : 1-101

746 atoms, 761 bonds, 101 residues, 1 model selected  

> color sel dark turquoise

> select clear

> hide #!1 models

> show #!1 models

> save /Volumes/Anindito/P1/tail/sheath_normal/new/session_fit_whole.cxs

——— End of log from Wed May 10 14:32:25 2023 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
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: MacBook Air
      Model Identifier: Mac15,12
      Model Number: MXCU3LL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.81.1
      OS Loader Version: 10151.81.1

Software:

    System Software Overview:

      System Version: macOS 14.3 (23D2057)
      Kernel Version: Darwin 23.3.0
      Time since boot: 57 days, 8 hours, 58 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      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: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    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-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-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: 1.8rc202406102315
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    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-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    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-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-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
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    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: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    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
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    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
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

[Eric Pettersen]

Reported by Anindito Sen

[Tom Goddard]

The error message indicates your MRC file has invalid header data. What software wrote that file? Apparently it tried to use the MRC symmetry information header field to put different non-symmetry data into the file. ChimeraX expects the symmetry information to follow the MRC specification and the program that wrote that file is abusing the file format.

When you open the session there is an error because a map file is not found (possibly this one with invalid symmetry information) and its surface was being colored based on radius. There is a bug in the ChimeraX code when it tries to report that the surface is missing. I fixed that bug in the ChimeraX daily build last week. So get the daily build so that you can open this session file with the missing map.