Crash in _cleanup

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-25-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007fc88caa4640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1284 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8ad7fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8adffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8ae7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/selectors.py", line 416 in select
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8aeffd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8af7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8affff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8d0ff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8d17fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8d1ffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8d27fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fc8d2ffd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007fc9c8fc5740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 359 in _cleanup
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 396 in cb
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connection.py", line 174, in _new_conn  
conn = connection.create_connection(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/util/connection.py", line 96, in create_connection  
raise err  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/util/connection.py", line 86, in create_connection  
sock.connect(sa)  
ConnectionRefusedError: [Errno 111] Connection refused  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 699, in urlopen  
httplib_response = self._make_request(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 394, in _make_request  
conn.request(method, url, **httplib_request_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connection.py", line 239, in request  
super(HTTPConnection, self).request(method, url, body=body, headers=headers)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1257, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1303, in
_send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1252, in
endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1012, in
_send_output  
self.send(msg)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 952, in send  
self.connect()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connection.py", line 205, in connect  
conn = self._new_conn()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connection.py", line 186, in _new_conn  
raise NewConnectionError(  
urllib3.exceptions.NewConnectionError: : Failed to establish a new connection: [Errno 111]
Connection refused  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1502, in on_finish  
versions = self.result.get()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 771,
in get  
raise self._value  
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 125,
in worker  
result = (True, func(*args, **kwds))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 233, in GET  
return self.request("GET", url,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 206, in request  
r = self.pool_manager.request(method, url,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/urllib3/request.py",
line 74, in request  
return self.request_encode_url(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/urllib3/request.py",
line 96, in request_encode_url  
return self.urlopen(method, url, **extra_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/poolmanager.py", line 375, in urlopen  
response = conn.urlopen(method, u.request_uri, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 755, in urlopen  
retries = retries.increment(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url:
/cxservices/api/v1//chimerax/newer?uuid=adc36d7b-fdaa-5353-9fff-479a6968a256&OS=%7Bsystem%7D+%7Blike%7D&OSVersion=22.04&ChimeraXVersion=1.3
(Caused by NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection
refused'))  
  
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url:
/cxservices/api/v1//chimerax/newer?uuid=adc36d7b-fdaa-5353-9fff-479a6968a256&OS=%7Bsystem%7D+%7Blike%7D&OSVersion=22.04&ChimeraXVersion=1.3
(Caused by NewConnectionError(': Failed to establish a new connection: [Errno
111] Connection refused'))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
  
See log for complete Python traceback.  
  

> open "/home/francesco/Desktop/2022/PAS_DOMAIN_2.1/PASDOMAIN_ongoing/single
> cluster nodes/PAS_domain_structures/AHR_PASA_domain.pdb"

AHR_PASA_domain.pdb title:  
Alphafold V2.0 prediction for aryl hydrocarbon receptor (P35869) [more
info...]  
  
Chain information for AHR_PASA_domain.pdb #1  
---  
Chain | Description | UniProt  
A | aryl hydrocarbon receptor | AHR_HUMAN  
  

> open "/home/francesco/Desktop/2022/PAS_DOMAIN_2.1/PASDOMAIN_ongoing/single
> cluster nodes/PAS_domain_structures/AHRR_PAS_domain.pdb"

AHRR_PAS_domain.pdb title:  
Alphafold V2.0 prediction for aryl hydrocarbon receptor repressor (A9YTQ3)
[more info...]  
  
Chain information for AHRR_PAS_domain.pdb #2  
---  
Chain | Description | UniProt  
A | aryl hydrocarbon receptor repressor | AHRR_HUMAN  
  

> open "/home/francesco/Desktop/2022/PAS_DOMAIN_2.1/PASDOMAIN_ongoing/single
> cluster nodes/PAS_domain_structures/NPAS4_PASA_domain.pdb"

NPAS4_PASA_domain.pdb title:  
Alphafold V2.0 prediction for neuronal pas domain-containing protein 4
(Q8IUM7) [more info...]  
  
Chain information for NPAS4_PASA_domain.pdb #3  
---  
Chain | Description | UniProt  
A | neuronal pas domain-containing protein 4 | NPAS4_HUMAN  
  

> ui tool show AlphaFold

> alphafold match #1

1 AlphaFold model found using UniProt identifier: P35869 (chain A)  
AlphaFold chains matching AHR_PASA_domain.pdb  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
A | AHR_HUMAN | P35869 | 0.00 | 848 | 147 | 100  
  
Opened 1 AlphaFold model  

> undo

> close session


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 22.1.7 - kisak-mesa PPA
OpenGL renderer: AMD Radeon Vega 11 Graphics (raven, LLVM 14.0.6, DRM 3.42, 5.15.0-25-generic)
OpenGL vendor: AMD
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B450M DS3H
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 AMD Ryzen 5 2400G with Radeon Vega Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            29Gi       8.7Gi        11Gi       295Mi       9.1Gi        19Gi
	Swap:          975Mi       441Mi       534Mi

Graphics:
	07:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Raven Ridge [Radeon Vega Series / Radeon Vega Mobile Series] [1002:15dd] (rev c6)	
	Subsystem: Advanced Micro Devices, Inc. [AMD/ATI] Raven Ridge [Radeon Vega Series / Radeon Vega Mobile Series] [1002:15dd]	
	Kernel driver in use: amdgpu
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[pett]

We no longer use _cleanup