Save MRC: could not broadcast input array

[zeyu.chen@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:/edge download/cryosparc_P769_J403_005_volume_map_sharp.mrc"

Opened cryosparc_P769_J403_005_volume_map_sharp.mrc as #1, grid size
380,380,380, pixel 0.725, shown at level 0.036, step 2, values float32  

> volume #1 level 0.1235

> volume #1 step 1

> volume flip #1

Opened cryosparc_P769_J403_005_volume_map_sharp.mrc z flip as #2, grid size
380,380,380, pixel 0.725, shown at step 1, values float32  

> close #1

> open
> D:/project/Roche/GPCR/GIPR/phenix/RealSpaceRefine_3/GIPR_EX3835_J348_real_space_refined_003.pdb

Chain information for GIPR_EX3835_J348_real_space_refined_003.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
E | No description available  
G | No description available  
R | No description available  
  

> hide atoms

> show cartoons

> transparency 50

> surface dust #2 size 7.25

> select add #1

9574 atoms, 9792 bonds, 9 pseudobonds, 1221 residues, 2 models selected  

> surface dust #2 size 7.25

> select subtract #1

Nothing selected  

> color zone #2 near #1 distance 4.35

> hide #!1 models

> transparency 0

> ui tool show "Color Zone"

> color zone #2 near #1 distance 3

> transparency 0

> color zone #2 near #1 distance 2

> color zone #2 near #1 distance 2.5

[Repeated 1 time(s)]

> transparency 0

> color zone #2 near #1 distance 2.8

> transparency 0

> color zone #2 near #1 distance 3

> transparency 0

> hide #!2 models

> show #!1 models

> select /G

453 atoms, 459 bonds, 59 residues, 1 model selected  

> color sel orange red

> select add #1

9574 atoms, 9792 bonds, 9 pseudobonds, 1221 residues, 2 models selected  

> show #!2 models

> color zone #2 near #1 distance 3

> hide #!1 models

> select subtract #1

Nothing selected  

> transparency 0

> color zone #2 near #1 distance 3.5

> transparency 0

> save "D:/project/Roche/GPCR/GIPR/model building/EX3835/J403/p769j403.mrc"
> models #2

> save "D:/project/Roche/GPCR/GIPR/model
> building/EX3835/J403/GIPR_EX3835_J403.pdb" relModel #2

> set bgColor white

> ui tool show "Color Zone"

> color single #2

> transparency 0

> show #!1 models

> transparency 50

> select add #1

9574 atoms, 9792 bonds, 9 pseudobonds, 1221 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.9958,0.058439,-0.070522,1.695,-0.063786,0.99506,-0.07612,19.565,0.065725,0.080298,0.9946,-19.64

> fitmap #1 inMap #2

Fit molecule GIPR_EX3835_J348_real_space_refined_003.pdb (#1) to map
p769j403.mrc (#2) using 9574 atoms  
average map value = 0.132, steps = 88  
shifted from previous position = 0.807  
rotated from previous position = 5.16 degrees  
atoms outside contour = 5106, contour level = 0.12348  
  
Position of GIPR_EX3835_J348_real_space_refined_003.pdb (#1) relative to
p769j403.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99193161 0.12529928 -0.01928142 -14.57822552  
-0.12601358 0.99114500 -0.04185899 24.29185956  
0.01386578 0.04395097 0.99893746 -7.71746476  
Axis 0.32064158 -0.12385941 -0.93906753  
Axis point 183.41597760 127.04236757 0.00000000  
Rotation angle (degrees) 7.68980134  
Shift along axis -0.43594013  
  

> select subtract #1

Nothing selected  

> ui tool show "Color Zone"

> color zone #2 near #1 distance 3

> transparency 0

> graphics silhouettes true

> hide #!1 models

> color single #2

> transparency 0

> show #!1 models

> transparency 50

> close #1-2

> set bgColor black

> set bgColor transparent

> open D:/project/Roche/GPCR/GIPR/202511_Roche_GIPR-
> EX3835_3.1A/cryosparc_P769_J403_005_volume_map.mrc

Opened cryosparc_P769_J403_005_volume_map.mrc as #1, grid size 380,380,380,
pixel 0.725, shown at level 0.0292, step 2, values float32  

> volume flip #1

Opened cryosparc_P769_J403_005_volume_map.mrc z flip as #2, grid size
380,380,380, pixel 0.725, shown at step 1, values float32  

> close #1

> save D:/project/Roche/GPCR/GIPR/202511_Roche_GIPR-
> EX3835_3.1A/cryosparc_P769_J403_005_volume_map.mrc models #2

Traceback (most recent call last):  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 185, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider  
what(session)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save  
show_save_file_dialog(session)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\\__init__.py", line 200, in save  
save_map(session, path, _name, **kw)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 4028, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_data\fileformats.py", line 326, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_data\mrc\writemrc.py", line 73, in
write_mrc2000_grid_data  
matrix = grid_data.matrix((0,0,k), (isz,jsz,1))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 39, in matrix  
m = self.data.matrix(origin, ijk_size, ijk_step, progress=progress,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_data\griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_data\mrc\mrc_grid.py", line 50, in read_matrix  
m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_data\mrc\mrc_format.py", line 287, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_data\readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: could not broadcast input array from shape (0,) into shape (380,)  
  
ValueError: could not broadcast input array from shape (0,) into shape (380,)  
  
File "E:\chimera X\chimeraX 1.10\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_data\readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.6556
OpenGL renderer: Intel(R) UHD Graphics 750
OpenGL vendor: Intel

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Vostro 3890
OS: Microsoft Windows 11 专业版 (Build 26100)
Memory: 34,067,255,296
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz
OSLanguage: zh-CN

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
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    build: 1.2.2.post1
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    ChimeraX-AddCharge: 1.5.19
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    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
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    ChimeraX-Dssp: 2.0
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    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[Tom Goddard]

This was fixed a month or two ago in the ChimeraX daily builds.

This error happens when you flip a map, close the original map, and then try to save the flipped map with the same file as the original map. ChimeraX is trying to read the data from the original map file to save the flipped version but that file is erased at the start of the save operation. I changed the code a while back so it saves to a temporary file to avoid this error.