id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14650 vop zone: ArrayMemoryError chimerax-bug-report@… Tom Goddard "{{{ 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 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 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 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 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 }}} " defect closed normal Volume Data limitation all ChimeraX