id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18832	ArrayMemoryError hiding atoms	chimerax-bug-report@…	Tom Goddard	"{{{
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
It took a lot of time to changes a molecular display. 

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/Admin/Downloads/4V60.cif

4V60.cif title:  
The structure of rat liver vault at 3.5 angstrom resolution [more info...]  
  
Chain information for 4V60.cif #1  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m | Major vault protein | MVP_RAT 1-861  
  
4V60.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> hide atoms

> show surfaces

> open ""7PKZ "" fromDatabase pdb format mmcif

PDB identifiers are either 4 or 8 characters long, got ""7PKZ ""  

> open ""7PKZ "" fromDatabase pdb format mmcif

PDB identifiers are either 4 or 8 characters long, got ""7PKZ ""  

> open 7PKZ fromDatabase pdb format mmcif

Summary of feedback from opening 7PKZ fetched from pdb  
---  
note | Fetching compressed mmCIF 7pkz from http://files.rcsb.org/download/7pkz.cif  
  
7pkz title:  
Vault structure in committed conformation [more info...]  
  
Chain information for 7pkz #2  
---  
Chain | Description | UniProt  
A AA AB AC B BA BB C CA CB D DA DB E EA EB F FA FB G GA GB H HA HB I IA IB J JA JB K KA KB L LA LB M MA MB N NA NB O OA OB P PA PB Q QA QB R RA RB S SA SB T TA TB UA UB V VA VB W WA WB X XA XB Y YA YB Z ZA ZB | Major vault protein | MVP_RAT 1-861  
  

> hide #!1 models

> close #1

> show surfaces

> hide atoms

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py"", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py"", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py"", line 1419, in run_provider  
return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py"", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py"", line 1394, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py"", line 403, in try_shortcut  
self.run_shortcut(keys)  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py"", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py"", line 340, in run  
f(s)  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py"", line 594, in run_expanded_command  
run(session, cmd)  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py"", line 537, in run  
run_command(session, command, **kw)  
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\std_commands\hide.py"", line 47, in hide  
atoms = objects.atoms  
^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\objects.py"", line 323, in atoms  
return all_atoms(self._session)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\structure.py"", line 2546, in all_atoms  
atoms = concatenate([m.atoms for m in structures], Atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molarray.py"", line 378, in concatenate  
p = numpy.concatenate([a._pointers for a in collections])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.66 MiB for an
array with shape (479700,) and data type uint64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.66 MiB for an
array with shape (479700,) and data type uint64  
  
File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molarray.py"", line 378, in concatenate  
p = numpy.concatenate([a._pointers for a in collections])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8729
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: LENOVO
Model: 81YA
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 4,195,586,048
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-8130U CPU @ 2.20GHz
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
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    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
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    ipykernel: 6.29.5
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}}}
"	defect	closed	normal		Core		limitation						all	ChimeraX