Clipper: ArrayMemoryError creating NXmapHandler

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> D:\\\REPAIRx\\\rfxcas13d_RNA_data\\\model_building\\\refine\\\J170_cas13d_RNA_rsr_coot-0-iso_rsr-
> iso_rsr-iso_rsr_rsr-coot-0_rsr.pdb

Chain information for J170_cas13d_RNA_rsr_coot-0-iso_rsr-iso_rsr-iso_rsr_rsr-
coot-0_rsr.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open D:/REPAIRx/rfxcas13d_RNA_data/em/J170_007_volume_map_em.mrc

Opened J170_007_volume_map_em.mrc as #2, grid size 256,256,256, pixel 1.06,
shown at level 0.072, step 1, values float32  

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB
standards.  
Chain information for J170_cas13d_RNA_rsr_coot-0-iso_rsr-iso_rsr-iso_rsr_rsr-
coot-0_rsr.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
  

> clipper associate #2 toModel #1

Traceback (most recent call last):  
File "C:\Users\yang\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\ui\general_tab\add_maps.py", line 64, in add_map_cb  
run(session, f'clipper assoc #{volume.id_string} to
#{session.isolde.selected_model.parent.id_string}')  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\yang\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\clipper\cmd.py", line 124, in associate_volumes  
mgr.nxmapset.add_nxmap_handler_from_volume(v)  
File "C:\Users\yang\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\clipper\maps\nxmapset.py", line 52, in
add_nxmap_handler_from_volume  
h = NXmapHandler(self, volume)  
File "C:\Users\yang\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\clipper\maps\nxmapset.py", line 157, in __init__  
super().__init__(mapset, name, data,  
File "C:\Users\yang\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\clipper\maps\map_handler_base.py", line 51, in __init__  
self._mean_sd_rms = self._full_mean_sd_rms()  
File "C:\Users\yang\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\clipper\maps\map_handler_base.py", line 56, in
_full_mean_sd_rms  
return mean_sd_rms(self.data.matrix())  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 3191, in mean_sd_rms  
sd = m.std(dtype=float64)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\numpy\core\\_methods.py", line 265, in _std  
ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\numpy\core\\_methods.py", line 233, in _var  
x = asanyarray(arr - arrmean)  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 128. MiB for an
array with shape (256, 256, 256) and data type float64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 128. MiB for an
array with shape (256, 256, 256) and data type float64  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\numpy\core\\_methods.py", line 233, in _var  
x = asanyarray(arr - arrmean)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 537.32
OpenGL renderer: NVIDIA GeForce RTX 3050 6GB Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 83AQ
OS: Microsoft Windows 11 家庭中文版 (Build 22631)
Memory: 16,907,100,160
MaxProcessMemory: 137,438,953,344
CPU: 16 13th Gen Intel(R) Core(TM) i5-13500H
OSLanguage: zh-CN

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[Tom Goddard]

I suspect this memory error is not caused by ISOLDE. There is a similar report in ChimeraX 1.6 and Windows 10 today #16405 and there have been many others always on Windows 10 that I think are related to an old fixed ChimeraX bug where reading mmCIF files sometimes ran out of memory.