Save surface in session: ArrayMemoryError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> E:/朱拯研一工作/20240709甲型流感病毒抗原抗体复合物结构分析/20241122文章记录及图片/3.抗原表位聚类/20241014保守表位及广谱抗体/HA/2/4fqr-3.cxs

Log from Sun Nov 24 17:16:51 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> E:/朱拯研一工作/20240709甲型流感病毒抗原抗体复合物结构分析/20241122文章记录及图片/3.抗原表位聚类/20241014保守表位及广谱抗体/HA/2/4fqr2.cxs

Log from Wed Oct 16 17:48:39 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "E:/朱拯研一工作/20240709甲型流感病毒抗原抗体复合物结构分析/influA epitope
> sim/贪心算法/相似性聚类/20241014保守表位及广谱抗体/HA/2/4fpr.cxs"

Log from Wed Oct 16 16:33:35 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:/朱拯研一工作/20240709甲型流感病毒抗原抗体复合物结构分析/influA epitope
> sim/贪心算法/相似性聚类/20241014保守表位及广谱抗体/HA/2/4fqr-pdb-bundle1.pdb"

Summary of feedback from opening E:/朱拯研一工作/20240709甲型流感病毒抗原抗体复合物结构分析/influA
epitope sim/贪心算法/相似性聚类/20241014保守表位及广谱抗体/HA/2/4fqr-pdb-bundle1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER VIRAL PROTEIN/IMMUNE SYSTEM 2012-06-25 XXXX  
  
Chain information for 4fqr-pdb-bundle1.pdb #1  
---  
Chain | Description  
A C E G I K M O Q S U W | No description available  
B D F H J L N P R T V X | No description available  
a c e g i k m o q s u w | No description available  
b d f h j l n p r t v x | No description available  
  
2376 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide cartoons

> hide atoms

> select /A

2466 atoms, 2523 bonds, 319 residues, 1 model selected  

> show sel cartoons

> surface sel

> color (#!1 & sel) light gray

> select :98,131,133,135,136,137,145,153,156,186,189,190,193,194,226,228

4824 atoms, 4452 bonds, 636 residues, 1 model selected  

> color (#!1 & sel) cornflower blue

> save "E:/朱拯研一工作/20240709甲型流感病毒抗原抗体复合物结构分析/influA epitope
> sim/贪心算法/相似性聚类/20241014保守表位及广谱抗体/HA/2/4fpr.cxs"

——— End of log from Wed Oct 16 16:33:35 2024 ———

opened ChimeraX session  

> graphics silhouettes true

> lighting shadows false

> lighting full

> lighting shadows false

> save C:/Users/Administrator/Desktop/4fqr2.cxs

——— End of log from Wed Oct 16 17:48:39 2024 ———

opened ChimeraX session  

> select /B

1405 atoms, 1429 bonds, 173 residues, 1 model selected  

> show sel surfaces

> color (#!1 & sel) light gray

> select clear

> save C:/Users/Administrator/Desktop/4fqr-3.bmp width 957 height 605
> supersample 3

> save C:/Users/Administrator/Desktop/4fqr-3.cxs

——— End of log from Sun Nov 24 17:16:51 2024 ———

opened ChimeraX session  

Invalid texture upload for 0x1b3bd775b30 layer=0 mip=0  

[Repeated 4 time(s)]

> save C:/Users/Administrator/Desktop/4fqr-3.cxs

Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\state.py", line 220, in _copy  
return data.copy()  
^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 2.21 MiB for an
array with shape (192820, 3) and data type float32  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001B39D599810> -> <chimerax.atomic.molsurf.MolecularSurface object at
0x000001B3D2769DD0> '4fqr-pdb-bundle1.pdb_A SES surface': Unable to allocate
2.21 MiB for an array with shape (192820, 3) and data type float32  
  
ValueError: error processing: 'models' -> -> '4fqr-pdb-bundle1.pdb_A SES
surface': Unable to allocate 2.21 MiB for an array with shape (192820, 3) and
data type float32  
  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\state.py", line 220, in _copy  
return data.copy()  
^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 2.21 MiB for an
array with shape (192820, 3) and data type float32  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001B39D599810> -> <chimerax.atomic.molsurf.MolecularSurface object at
0x000001B3D2769DD0> '4fqr-pdb-bundle1.pdb_A SES surface': Unable to allocate
2.21 MiB for an array with shape (192820, 3) and data type float32  
  
ValueError: error processing: 'models' -> -> '4fqr-pdb-bundle1.pdb_A SES
surface': Unable to allocate 2.21 MiB for an array with shape (192820, 3) and
data type float32  
  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save C:/Users/Administrator/Desktop/4fqr-3.cxs

Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 219, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 2021, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: exception: access violation writing 0x0000000000000000  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x000001B39D599810> ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x000001B3DD818650> '4fqr-
pdb-bundle1.pdb_B SES surface' -> <chimerax.atomic.structure.AtomicStructure
object at 0x000001B3E2949E10> '4fqr-pdb-bundle1.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001B39D599810> -> <chimerax.atomic.molsurf.MolecularSurface object at
0x000001B3DD818650> '4fqr-pdb-bundle1.pdb_B SES surface' ->
<chimerax.atomic.structure.AtomicStructure object at 0x000001B3E2949E10>
'4fqr-pdb-bundle1.pdb': Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x000001B39D599810> ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x000001B3DD818650> '4fqr-
pdb-bundle1.pdb_B SES surface' -> <chimerax.atomic.structure.AtomicStructure
object at 0x000001B3E2949E10> '4fqr-pdb-bundle1.pdb'  
  
ValueError: error processing: 'models' -> -> '4fqr-pdb-bundle1.pdb_B SES
surface' -> '4fqr-pdb-bundle1.pdb': Error while saving session data for
'models' -> -> '4fqr-pdb-bundle1.pdb_B SES surface' -> '4fqr-pdb-bundle1.pdb'  
  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1418, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 219, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 2021, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: exception: access violation writing 0x0000000000000000  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x000001B39D599810> ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x000001B3DD818650> '4fqr-
pdb-bundle1.pdb_B SES surface' -> <chimerax.atomic.structure.AtomicStructure
object at 0x000001B3E2949E10> '4fqr-pdb-bundle1.pdb'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save  
mgr.discovery(self._state_containers)  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001B39D599810> -> <chimerax.atomic.molsurf.MolecularSurface object at
0x000001B3DD818650> '4fqr-pdb-bundle1.pdb_B SES surface' ->
<chimerax.atomic.structure.AtomicStructure object at 0x000001B3E2949E10>
'4fqr-pdb-bundle1.pdb': Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x000001B39D599810> ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x000001B3DD818650> '4fqr-
pdb-bundle1.pdb_B SES surface' -> <chimerax.atomic.structure.AtomicStructure
object at 0x000001B3E2949E10> '4fqr-pdb-bundle1.pdb'  
  
ValueError: error processing: 'models' -> -> '4fqr-pdb-bundle1.pdb_B SES
surface' -> '4fqr-pdb-bundle1.pdb': Error while saving session data for
'models' -> -> '4fqr-pdb-bundle1.pdb_B SES surface' -> '4fqr-pdb-bundle1.pdb'  
  
File "G:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 537.34
OpenGL renderer: NVIDIA GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: FX503VD
OS: Microsoft Windows 10 专业版 (Build 18362)
Memory: 8,468,484,096
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

[Tom Goddard]

Duplicate of #16365