Out of memory converting Gromacs list of numpy coords to 2D numpy array

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
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 C:/Users/Jzhan/Desktop/Apple/JLab/PcUGT1/md_0_10.gro

Summary of feedback from opening
C:/Users/Jzhan/Desktop/Apple/JLab/PcUGT1/md_0_10.gro  
---  
note | Singleton residues assigned chain ID B  
  
Chain information for Protein in water #1  
---  
Chain | Description  
A | No description available  
  

> select solvant

Expected an objects specifier or a keyword  

> select water

Expected an objects specifier or a keyword  

> select solvent

407538 atoms, 271684 bonds, 135854 residues, 1 model selected  

> delete sel

> show cartoons

> style sphere

Changed 7949 atom styles  

> hide cartoons

> hide atoms

> show atoms

> sphere hide

Unknown command: sphere hide  

> style stick

Changed 7949 atom styles  

> show cartoons

> select side chain

Expected an objects specifier or a keyword  

> select sidechain

5907 atoms, 5483 bonds, 498 residues, 1 model selected  

> delete sel

> open C:/Users/Jzhan/Desktop/Apple/JLab/PcUGT1/md_0_10_center.xtc

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 768, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2154, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\md_crds\\__init__.py", line 118, in open  
num_coords = read_coords(session, data, structure_model, md_type,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 40, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 9.30 GiB for an
array with shape (1001, 415487, 3) and data type float64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 9.30 GiB for an
array with shape (1001, 415487, 3) and data type float64  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 40, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 24.20.100.6293
OpenGL renderer: Intel(R) HD Graphics 520
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: Microsoft Corporation
Model: Surface Book
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 8,503,255,040
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6300U CPU @ 2.40GHz
OSLanguage: zh-CN

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[Eric Pettersen]

This conversion uses 2x the memory it really needs. gromacs.cpp should directly create the 2D array.