volume splitbyzone: ArrayMemoryError

[parthodas@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9rc202410300406 (2024-10-30 04:06:08 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202410300406 (2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\parth\Downloads\cryosparc_P16_J227_003_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P16_J227_003_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.92, shown at level 0.182, step 2, values float32  

> volume #1 step 1

> set bgColor white

> volume flip #1 axis z

Opened cryosparc_P16_J227_003_volume_map_sharp.mrc z flip as #2, grid size
400,400,400, pixel 0.92, shown at step 1, values float32  

> close #1

> volume #2 color #919191

> set bgColor white

> graphics silhouettes true

> open C:/Users/parth/Downloads/4p1y.pdb

4p1y.pdb title:  
Crystal structure of staphylococcal γ-hemolysin prepore [more info...]  
  
Chain information for 4p1y.pdb #1  
---  
Chain | Description | UniProt  
A C E G | LUKF | Q931F3_STAAM 2-300  
B D F H | γ-hemolysin component A | HLGA_STAAM 13-280  
  

> ui mousemode right "translate selected models"

Drag select of 34011 atoms, 12 pseudobonds  

> view matrix models #1,1,0,0,174.05,0,1,0,116.72,0,0,1,-22.391

> view matrix models #1,1,0,0,223.22,0,1,0,137.18,0,0,1,267.93

> view matrix models #1,1,0,0,228.55,0,1,0,139.33,0,0,1,265.09

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.8449,-0.53073,0.066938,247.64,0.52109,0.84485,0.12124,174.18,-0.1209,-0.067554,0.99036,262.3

> fitmap #1 inMap #2

Fit molecule 4p1y.pdb (#1) to map cryosparc_P16_J227_003_volume_map_sharp.mrc
z flip (#2) using 34011 atoms  
average map value = 0.1675, steps = 112  
shifted from previous position = 8.4  
rotated from previous position = 10.2 degrees  
atoms outside contour = 19523, contour level = 0.18172  
  
Position of 4p1y.pdb (#1) relative to
cryosparc_P16_J227_003_volume_map_sharp.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.90228263 -0.43114505 -0.00008249 249.43489782  
0.43114504 0.90228263 -0.00011042 161.28248239  
0.00012204 0.00006406 0.99999999 270.64265331  
Axis 0.00020235 -0.00023719 0.99999995  
Axis point -231.25393629 630.82635392 0.00000000  
Rotation angle (degrees) 25.54025071  
Shift along axis 270.65485806  
  

> hide sel atoms

> show sel cartoons

> select clear

> color #1 #9f9feeff

> ui tool show "Color Zone"

> color zone #2 near #1 distance 5.52

> volume splitbyzone #2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\surface\colorzonegui.py", line 253, in _split_map  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 378, in
split_volumes_by_color_zone  
vlist.extend(split_volume_by_color_zone(v))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 321, in
split_volume_by_color_zone  
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 362, in split_zones_by_color  
g = masked_grid_data(sg, mask, m)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\map_data\arrays.py", line 345, in masked_grid_data  
putmask(masked, mask == mask_value, matrix)  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an
array with shape (400, 400, 400) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an
array with shape (400, 400, 400) and data type float32  
  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\map_data\arrays.py", line 345, in masked_grid_data  
putmask(masked, mask == mask_value, matrix)  
  
See log for complete Python traceback.  
  

> fitmap #1 inMap #2

Fit molecule 4p1y.pdb (#1) to map cryosparc_P16_J227_003_volume_map_sharp.mrc
z flip (#2) using 34011 atoms  
average map value = 0.1675, steps = 28  
shifted from previous position = 0.0239  
rotated from previous position = 0.0201 degrees  
atoms outside contour = 19517, contour level = 0.18172  
  
Position of 4p1y.pdb (#1) relative to
cryosparc_P16_J227_003_volume_map_sharp.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.90219684 -0.43132453 0.00014795 249.46435436  
0.43132455 0.90219679 -0.00028491 161.28689697  
-0.00001059 0.00032086 0.99999995 270.62846817  
Axis 0.00070222 0.00018379 0.99999974  
Axis point -230.90108180 630.28417987 0.00000000  
Rotation angle (degrees) 25.55165540  
Shift along axis 270.83321841  
  

> surface dust #2 size 9.2

> color zone #2 near #1 distance 5.52

> volume splitbyzone #2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\surface\colorzonegui.py", line 253, in _split_map  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 378, in
split_volumes_by_color_zone  
vlist.extend(split_volume_by_color_zone(v))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 321, in
split_volume_by_color_zone  
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 362, in split_zones_by_color  
g = masked_grid_data(sg, mask, m)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\map_data\arrays.py", line 341, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an
array with shape (400, 400, 400) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an
array with shape (400, 400, 400) and data type float32  
  
File "C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site-
packages\chimerax\map_data\arrays.py", line 341, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8681
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: VivoBook_ASUSLaptop X409FA_X409FA
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 8,434,266,112
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
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    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
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    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

[Eric Pettersen]

Reported by Partho

[Tom Goddard]

This ChimeraX error says it ran out of memory running "volume splitbyzone". I'm a bit surprised since it was only trying to make two copies of your 400 x 400 x 400 map for the region near 4p1y and the region far away which would only use 0.5 GB. Your machine has little memory at 8 GB but it should be enough. Unfortunately we often see these out of memory errors on Windows. It may be worth updating to ChimeraX 1.9 since some memory leaks reading mmCIF files were fixed a while back, although I think your version has those fixes. So I don't have any suggestion to help you other than use a computer with more memory.