Save MRC file: could not broadcast input array from shape

[haaris.safdari@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> mousemode shift leftMode "translate selected models"

> mousemode shift middleMode "rotate selected models"

> mousemode rightMode zoom

> mousemode control wheelMode "contour level"

> mousemode setting "contour level" speed 0.1

> mousemode shift wheelMode "rotate selected models"

> camera ortho

> set bgColor grey

> lighting shadows false

> lighting depthCue false

> graphics silhouettes true

> lighting simple

> functionkey F1 cofr sel

> functionkey F2 mousemode rightMode 'mark surface'

> functionkey F3 mousemode rightMode 'move markers'

> functionkey F4 mk 3 1

> functionkey F5 view

> functionkey F6 view sel pad 0.92 clip false

> functionkey F7 mousemode rightMode 'delete markers'

> functionkey F8 mousemode rightMode zoom

> functionkey F9 sequence chain sel

> functionkey F10 transparency sel 65

> functionkey F11 transparency sel 0

> functionkey F12 tool show 'Fit in Map'

> color name f01graublau #BADBED

Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed

  

> color name f02silber #F6FAFC

Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc

  

> color name f03muschel #FFFFE5

Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5

  

> color name f04beige #F3F3A9

Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9

  

> color name f05gelb #f2b701

Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701

  

> color name f06orange #e68310

Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310

  

> color name f07rotorange #FF6A25

Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25

  

> color name f08rot #dd3d2d

Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d

  

> color name f09lachs #f97b72

Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72

  

> color name f10flieder #D57AD5

Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5

  

> color name f11violett #cf1c90

Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90

  

> color name f12lila #4b148f

Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f

  

> color name f13dunkelblau #2E2EF7

Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7

  

> color name f14blau #00AAFF

Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff

  

> color name f15cyan #60e2d6

Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6

  

> color name f16blaugrün #30ffa6

Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6

  

> color name f17grün #00FF00

Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00

  

> color name f18dunkelgrün #228B22

Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  

> color name f19hellgrau #DCDCDC

Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc

  

> color name f20grau #B2B2B2

Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2

  

> color name f21anthrazit #323F45

Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45

  

> alias localres color sample #$1 map #$2 offset 0.1 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4

> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'

> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'

> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3

> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3

> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3

> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow

> alias chaininfo preset custom chaininfo

> alias foto save browse format tiff height 4000 supersample 4
> transparentBackground false

> alias durch save browse format tiff height 4000 supersample 4
> transparentBackground true

> alias session save browse format session includeMaps true compress lz4

> alias nomapsession save browse format session includeMaps false compress lz4

> alias splitup color zone #$1 near sel sharpEdges true distance $2

> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2

> alias spalt volume splitbyzone #$1

> alias undust surface undust #$1

> alias dust1 surface dust #$1 size 1

> alias dust2 surface dust #$1 size 2

> alias dust3 surface dust #$1 size 3

> alias dust4 surface dust #$1 size 4

> alias dust5 surface dust #$1 size 5

> alias dust6 surface dust #$1 size 6

> alias dust7 surface dust #$1 size 7

> alias dust8 surface dust #$1 size 8

> alias dust9 surface dust #$1 size 9

> alias dust10 surface dust #$1 size 10

> alias dust11 surface dust #$1 size 11

> alias dust12 surface dust #$1 size 12

> alias dust13 surface dust #$1 size 13

> alias dust14 surface dust #$1 size 14

> alias dust15 surface dust #$1 size 15

> alias dust20 surface dust #$1 size 20

> alias dust25 surface dust #$1 size 25

> alias dust30 surface dust #$1 size 30

> alias dust35 surface dust #$1 size 35

> alias dust40 surface dust #$1 size 40

> alias dust45 surface dust #$1 size 45

> alias dust50 surface dust #$1 size 50

> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> "#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"
> range $3,$4

> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true

> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true

> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho

UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Haaris/Desktop/MTX_50uM/run_class001.mrc

File size 1024 too small for grid size (500,500,500)  

> open /Users/Haaris/Desktop/MTX_50uM/run_class001.LessEFG.mrc

Opened run_class001.LessEFG.mrc as #1, grid size 500,500,500, pixel 0.85,
shown at level 0.0111, step 2, values float32  

> volume flip #1

Opened run_class001.LessEFG.mrc z flip as #2, grid size 500,500,500, pixel
0.85, shown at step 1, values float32  

> hide #!2 models

> show #!2 models

> close #1

> save /Users/Haaris/Desktop/MTX_50uM/run_class001.LessEFG.mrc models #2

Traceback (most recent call last):  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save  
save_map(session, path, _name, **kw)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/writemrc.py", line 68, in
write_mrc2000_grid_data  
matrix = grid_data.matrix((0,0,k), (isz,jsz,1))  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_filter/flip.py", line 37, in read_matrix  
m = self.data.matrix(origin, ijk_size, ijk_step, progress)  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 57, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
ValueError: could not broadcast input array from shape (0,) into shape (500,)  
  

Populating font family aliases took 252 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

ValueError: could not broadcast input array from shape (0,) into shape (500,)  
  
File
"/Users/Haaris/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/readarray.py", line 57, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3,7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      System Firmware Version: 1731.140.1.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 27 days 19:45

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 0FFXD31242JL
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
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[Tom Goddard]

This error saving an MRC file is because the original map file whose z-flipped version was being copied was overwritten by the time you tried to save and the save required rereading the original file.

ChimeraX does not read the full map file when you open it unless you it needs to. This makes ChimeraX respond faster by avoiding reading large files unnecessarily. But because the reading can be delayed, if the file changes on disk after it was opened it can cause errors when ChimeraX later tries to read it.

In your case here is what happened. You opened run_class001.LessEFG.mrc which displayed at step size 2, so only every other plane of the file was read. Then it was z flipped. The z-flipped version showed the data a full resolution, so the original map was entirely read. But then you closed the original map in ChimeraX and that cleared the cache of that read in data. So when you tried to save the flipped map it tried to reread the original map file. But that file had been overwritten and was too small so the read failed.

[Tom Goddard]

This is a very rare error but I have seen it reported maybe once a year. It would be possible to have ChimeraX check if the file has changed since it was originally opened and give a clear error message that says the file changed and ChimeraX was trying to reread it. I don't think it is worth the coding effort to put in this better error reporting since it is a very rare error, but maybe I will in the future.