Cannot show tomogram as surface or volume

[weijianz@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-100-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Mrc tomograms can be opened in default "plane" mode but can not be transformed into "surface" or " volume" or any other volume viewing mode. 

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /media/chiulab/S/li/segmentations/C1_05_rec.lih_lp100.mrc

Opened C1_05_rec.lih_lp100.mrc as #1, grid size 1024,1440,425, pixel
8.53,8.53,8.53, shown at step 1, values float32  

> volume #1 region 0,0,0,1023,1439,424 step 4

[Repeated 1 time(s)]Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 4010, in _update_drawings  
v.update_drawings()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 777, in update_drawings  
levels, colors = self.initial_surface_levels()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 578, in initial_surface_levels  
mstats = self.matrix_value_statistics()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1708, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix  
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 55, in read_array  
data = file.read(ibytes)  
OSError: [Errno 5] Input/output error  
  
Error processing trigger "graphics update":  
OSError: [Errno 5] Input/output error  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 55, in read_array  
data = file.read(ibytes)  
  
See log for complete Python traceback.  
  

> volume #1 change image level -3.03e-12,0 level 8.178e-09,0.8 level
> 1.994e-08,1

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2146, in mousePressEvent  
cb(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2209, in select_data_cb  
d.redisplay_needed_cb()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 362, in
show_using_dialog_settings  
dr.show()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 748, in show  
self._keep_displayed_data = self.displayed_matrices() if show else None  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 44, in read_matrix  
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 284, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 55, in read_array  
data = file.read(ibytes)  
OSError: [Errno 5] Input/output error  
  
OSError: [Errno 5] Input/output error  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 55, in read_array  
data = file.read(ibytes)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Silicon Mechanics
Model: Workform 2000
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 48 Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
Cache Size: 30720 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi       2.0Gi       120Gi        22Mi       3.6Gi       122Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)	
	Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
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    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
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    ChimeraX-ShowAttr: 1.0
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    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
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    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
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    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
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    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
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    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
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    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
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    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

Reported by Albert Zhou

[Tom Goddard]

The error message means the file was not readable.

OSError: [Errno 5] Input/output error

Possibly the file was deleted after opening it. ChimeraX does not read the full file when you open it, and if you change the step size will read just the part of the file it needs. So if you open it, then delete or rename it, then change the step size for display you can get this type of file reading error.

Let me know if that is not the cause.