Opened 20 months ago

Closed 20 months ago

#14650 closed defect (limitation)

vop zone: ArrayMemoryError

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\Administrator\\\Desktop\\\PLO-
> COL_J1170-ABUV-039-coot-3rd.pdb

Chain information for PLO-COL_J1170-ABUV-039-coot-3rd.pdb #1  
---  
Chain | Description  
A B | No description available  
U V | No description available  
  

> open C:\\\Users\\\Administrator\\\Desktop\\\J1170_UDP_galactose_sharp.mrc

Opened J1170_UDP_galactose_sharp.mrc as #2, grid size 384,384,384, pixel 1.1,
shown at level 0.168, step 2, values float32  

> volume #2 step 1

> set bgColor white

> volume style mesh

[Repeated 1 time(s)]

> surface dust #2 size 11

> hide cartoons

> hide atoms

> volume hide

> show #1/B:337-353

> select #1/B:337-353

146 atoms, 153 bonds, 17 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #3, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> view clip false

> color sel red

> color sel byhetero

> color #2 black models

> color #3 black models

> select clear

> ui mousemode right "color key"

> ui mousemode right translate

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> save C:\Users\Administrator/Desktop\image1.png supersample 3

[Repeated 1 time(s)]

> hide cartoons

> hide atoms

> volume #!3 hide

> show #1/B:325-327

> select clear

> color #1 red

> color #1 byhetero

> select #1/B:325-327

26 atoms, 26 bonds, 3 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #5, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #5 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> show atoms

> hide atoms

> volume #!5 hide

> show #1/B:311-320

> select #1/B:311-320

89 atoms, 90 bonds, 10 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #6, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #6 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> show #1/B:259-266

> hide atoms

> volume #!6 hide

> show #1/B:259-266

> select #1/B:259-266

66 atoms, 66 bonds, 8 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #7, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #7 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!7 hide

> show #1/B:226-228

> select #1/B:226-228

25 atoms, 24 bonds, 3 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #8, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #8 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!8 hide

> select #1/B:202-208

56 atoms, 56 bonds, 7 residues, 1 model selected  

> show #1/B:202-208

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #9, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #9 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!9 hide

> select #1/B:191-200

94 atoms, 96 bonds, 10 residues, 1 model selected  

> show #1/B:191-200

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #10, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #10 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!10 hide

> show #1/B:173-182

> select #1/B:173-182

81 atoms, 81 bonds, 10 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #11, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #11 black models

> select clear

> hide atoms

> volume #!11 hide

> show #!5 models

> hide #!5 models

> show #!3 models

> select #1/B:337-353

146 atoms, 153 bonds, 17 residues, 1 model selected  

> show #1/B:337-353

> select clear

> volume #3 level 0.2

> volume #3 level 0.3

> volume #3 level 0.4

> volume #3 level 0.35

> volume #3 level 0.4

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!3 hide

> show #1/B:325-327

> select #1/B:325-327

26 atoms, 26 bonds, 3 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #12, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> close #12

> show #!5 models

> volume all level 0.4

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!5 hide

> show #1/B:311-320

> show #!6 models

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!6 hide

> show #1/B:259-266

> hide atoms

> show #1/B:337-353

> show #!3 models

> hide #!3 models

> hide atoms

> show #1/B:259-266

> hide atoms

> show #1/B:325-327

> hide atoms

> show #1/B:311-320

> show #!5 models

> hide #!5 models

> show #!6 models

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide #!6 models

> hide atoms

> show #1/B:259-266

> show #!7 models

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!7 hide

> show #1/B:226-228

> hide atoms

> show #1/B:337-353

> show #!3 models

> hide #!3 models

> hide atoms

> show #1/B:325-327

> show #1/B:311-320

> show #1/B:259-266

> hide atoms

> show #1/B:259-266

> show #1/B:311-320

> show #1/B:259-266

> hide atoms

> show atoms

> hide atoms

> show #1/B:259-266

> hide atoms

> show #1/B:226-228

> show #!9 models

> hide #!9 models

> show #!8 models

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!8 hide

> show #1/B:202-208

> show #!8 models

> hide #!8 models

> show #!9 models

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!9 hide

> show #1/B:191-200

> show #!10 models

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!10 hide

> show #1/B:173-182

> show #!10 models

> hide #!10 models

> show #!11 models

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!11 hide

> show #1/B:149-153

> show #!11 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> select #1/B:149-153

35 atoms, 34 bonds, 5 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #4 color black

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!4 hide

> show #1/B:122-132

> select #1/B:122-132

90 atoms, 91 bonds, 11 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #12, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #12 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!12 hide

> show #1/B:88-100

> select #1/B:88-100

123 atoms, 125 bonds, 13 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #13, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #13 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!13 hide

> show #1/B:50-62

> select #1/B:50-62

116 atoms, 119 bonds, 13 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #14, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #14 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!14 hide

> show #1/B:36-38

[Repeated 2 time(s)]

> select #1/B:36-38

25 atoms, 25 bonds, 3 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #15, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #15 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!15 hide

> show #!3 models

> show #1/B:337-353

> hide atoms

> show atoms

> hide atoms

> volume #!3 hide

> show #1/B:362-364

> select #1/B:362-364

25 atoms, 25 bonds, 3 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #16, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #16 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!16 hide

> show #1/B:368-380

> select #1/B:368-380

98 atoms, 98 bonds, 13 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #17, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #17 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!17 hide

> show #1/B:337-353

> show #1/B:368-380

> hide atoms

> show #1/B:337-353

> select #1/B:337-353

146 atoms, 153 bonds, 17 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #18, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> close #18

> show #!3 models

> select clear

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide atoms

> show #1/B:362-364

> show #1/B:368-380

> hide atoms

> show #1/B:368-380

> select #1/B:368-380

98 atoms, 98 bonds, 13 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #18, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> show #!17 models

> close #18

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!17 hide

> show #1/B:402-409

> select #1/B:402-409

68 atoms, 67 bonds, 8 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #18, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> color #18 black models

> select clear

> save C:\Users\Administrator/Desktop\image1.png supersample 3

> hide atoms

> volume #!18 hide

> show #1/B:402-409

> hide atoms

> show #1/B:444-448

> select #1/B:444-448

43 atoms, 43 bonds, 5 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Traceback (most recent call last):  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2929, in run  
result = ci.function(session, *args, optional=optional,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3468, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1135, in volume_zone  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1135, in <listcomp>  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_filter\zone.py",
line 42, in zone_operation  
vz = zone_volume(v, points, radius, minimal_bounds, invert,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_filter\zone.py",
line 71, in zone_volume  
mg = map_data.zone_masked_grid_data(sg, points, radius, invert,
minimal_bounds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 275, in zone_masked_grid_data  
masked_data = masked_grid_data(grid_data, mask)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\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 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
File "D:\ChimeraX\ChimeraX\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.  
  

> vop zone #2 near sel range 1.7 newmap 1

Traceback (most recent call last):  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2929, in run  
result = ci.function(session, *args, optional=optional,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3468, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1135, in volume_zone  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1135, in <listcomp>  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_filter\zone.py",
line 42, in zone_operation  
vz = zone_volume(v, points, radius, minimal_bounds, invert,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_filter\zone.py",
line 71, in zone_volume  
mg = map_data.zone_masked_grid_data(sg, points, radius, invert,
minimal_bounds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 275, in zone_masked_grid_data  
masked_data = masked_grid_data(grid_data, mask)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\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 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
File "D:\ChimeraX\ChimeraX\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.  
  

> vop zone #2 near sel range 1.7 newmap 1

Traceback (most recent call last):  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2929, in run  
result = ci.function(session, *args, optional=optional,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3468, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1135, in volume_zone  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1135, in <listcomp>  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_filter\zone.py",
line 42, in zone_operation  
vz = zone_volume(v, points, radius, minimal_bounds, invert,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_filter\zone.py",
line 71, in zone_volume  
mg = map_data.zone_masked_grid_data(sg, points, radius, invert,
minimal_bounds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 275, in zone_masked_grid_data  
masked_data = masked_grid_data(grid_data, mask)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\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 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
File "D:\ChimeraX\ChimeraX\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.  
  

> vop zone #2 near sel range 1.7 newmap 1

Traceback (most recent call last):  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2929, in run  
result = ci.function(session, *args, optional=optional,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3468, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1135, in volume_zone  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1135, in <listcomp>  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_filter\zone.py",
line 42, in zone_operation  
vz = zone_volume(v, points, radius, minimal_bounds, invert,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_filter\zone.py",
line 71, in zone_volume  
mg = map_data.zone_masked_grid_data(sg, points, radius, invert,
minimal_bounds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 275, in zone_masked_grid_data  
masked_data = masked_grid_data(grid_data, mask)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\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 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
File "D:\ChimeraX\ChimeraX\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 NVIDIA 536.99
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Acer
Model: Predator PHN16-71
OS: Microsoft Windows 10 专业版 (Build 19044)
Memory: 16,886,128,640
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i5-13500HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 20 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → vop zone: ArrayMemoryError

comment:2 by Tom Goddard, 20 months ago

Resolution: → limitation
Status: assigned → closed

Error says numpy ran out of memory trying to allocate an 216 Mbyte array when using the newmap option of the "volume zone" command. Not clear why it ran out of memory. Windows 10 machine with 16 GB. Could give a clearer error message, but once you are close to out of memory the memory errors can happen anywhere so I don't think putting a message in this one place would help.

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