Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
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.
Windows fatal exception: code 0x8001010d

Thread 0x000033f0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004e0c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000036f8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004ee4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004d84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003c3c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004ec8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004e94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004ea4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004ef4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004f34 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00000b54 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1099 in read
  File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1241 in recv_into
  File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 704 in readinto
  File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 613 in _safe_read
  File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 472 in read
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\available.py", line 51 in load
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 456 in reload_available
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x000032e4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 699, in urlopen  
httplib_response = self._make_request(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 382, in _make_request  
self._validate_conn(conn)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 1010, in _validate_conn  
conn.connect()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connection.py", line 416, in connect  
self.sock = ssl_wrap_socket(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\ssl_.py", line 449, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\ssl_.py", line 493, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1309, in
do_handshake  
self._sslobj.do_handshake()  
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: certificate has expired (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1502, in on_finish  
versions = self.result.get()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
771, in get  
raise self._value  
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
125, in worker  
result = (True, func(*args, **kwds))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 233, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 206, in request  
r = self.pool_manager.request(method, url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 74, in request  
return self.request_encode_url(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 96, in request_encode_url  
return self.urlopen(method, url, **extra_kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 417, in urlopen  
return self.urlopen(method, redirect_location, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 375, in urlopen  
response = conn.urlopen(method, u.request_uri, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 755, in urlopen  
retries = retries.increment(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=3130c46a-d4ff-537f-bc23-1c4c59d0e7e1&OS=windows&OSVersion=10.0.19045&ChimeraXVersion=1.3
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired
(_ssl.c:1129)')))  
  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=3130c46a-d4ff-537f-bc23-1c4c59d0e7e1&OS=windows&OSVersion=10.0.19045&ChimeraXVersion=1.3
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired
(_ssl.c:1129)')))  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
  
See log for complete Python traceback.  
  
\--- Logging error ---  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\logging\\__init__.py", line 1086,
in emit  
stream.write(msg + self.terminator)  
AttributeError: 'NoneType' object has no attribute 'write'  
Call stack:  
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930, in
_bootstrap  
self._bootstrap_inner()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
125, in worker  
result = (True, func(*args, **kwds))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 233, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 206, in request  
r = self.pool_manager.request(method, url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 74, in request  
return self.request_encode_url(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 96, in request_encode_url  
return self.urlopen(method, url, **extra_kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 417, in urlopen  
return self.urlopen(method, redirect_location, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 375, in urlopen  
response = conn.urlopen(method, u.request_uri, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 780, in urlopen  
log.warning(  
Message: "Retrying (%r) after connection broken by '%r': %s"  
Arguments: (Retry(total=1, connect=None, read=None, redirect=None,
status=None), SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired
(_ssl.c:1129)')),
'/cxservices/api/v1/chimerax/newer?uuid=3130c46a-d4ff-537f-bc23-1c4c59d0e7e1&OS=windows&OSVersion=10.0.19045&ChimeraXVersion=1.3')  
\--- Logging error ---  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\logging\\__init__.py", line 1086,
in emit  
stream.write(msg + self.terminator)  
AttributeError: 'NoneType' object has no attribute 'write'  
Call stack:  
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930, in
_bootstrap  
self._bootstrap_inner()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
125, in worker  
result = (True, func(*args, **kwds))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 233, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 206, in request  
r = self.pool_manager.request(method, url,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 74, in request  
return self.request_encode_url(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 96, in request_encode_url  
return self.urlopen(method, url, **extra_kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 417, in urlopen  
return self.urlopen(method, redirect_location, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 375, in urlopen  
response = conn.urlopen(method, u.request_uri, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 780, in urlopen  
log.warning(  
Message: "Retrying (%r) after connection broken by '%r': %s"  
Arguments: (Retry(total=0, connect=None, read=None, redirect=None,
status=None), SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired
(_ssl.c:1129)')),
'/cxservices/api/v1/chimerax/newer?uuid=3130c46a-d4ff-537f-bc23-1c4c59d0e7e1&OS=windows&OSVersion=10.0.19045&ChimeraXVersion=1.3')  

> open C:/Users/eliferd/Downloads/P17_DewA_Alphafold_benchling.cif

Summary of feedback from opening
C:/Users/eliferd/Downloads/P17_DewA_Alphafold_benchling.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for MET /A:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for P17_DewA_Alphafold_benchling.cif #1  
---  
Chain | Description  
A | No description available  
  

> close session

> open "C:\Users\eliferd\OneDrive - Danmarks Tekniske
> Universitet\Skrivebord\Interfaces\Projects\Hydrophobins\17dew____.pdb"
> format pdb

Chain information for 17dew____.pdb #1  
---  
Chain | Description  
? | No description available  
  

> close session

> open C:/Users/eliferd/Downloads/Choline_Ox_WT_benchling.cif

Summary of feedback from opening
C:/Users/eliferd/Downloads/Choline_Ox_WT_benchling.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for MET /A:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Choline_Ox_WT_benchling.cif #1  
---  
Chain | Description  
A | No description available  
  

> close session

> open C:/Users/eliferd/Downloads/Choline_Oxidase_CO6_benchling.cif

Summary of feedback from opening
C:/Users/eliferd/Downloads/Choline_Oxidase_CO6_benchling.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for MET /A:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Choline_Oxidase_CO6_benchling.cif #1  
---  
Chain | Description  
A | No description available  
  

> show surfaces

> undo

> hide surfaces

> show cartoons

> color bychain

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Choline_Oxidase_CO6_benchling.cif_A SES surface #1.1:
minimum, -20.19, mean -2.81, maximum 10.85  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> open "C:\Users\eliferd\OneDrive - Danmarks Tekniske
> Universitet\Skrivebord\Interfaces\Projects\Hydrophobins\17dew____.pdb"
> format pdb

Chain information for 17dew____.pdb #1  
---  
Chain | Description  
? | No description available  
  

> close session

> open C:/Users/eliferd/Downloads/Choline_Ox_WT_benchling.cif

Summary of feedback from opening
C:/Users/eliferd/Downloads/Choline_Ox_WT_benchling.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for MET /A:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Choline_Ox_WT_benchling.cif #1  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/eliferd/Downloads/Choline_Oxidase_CO6_benchling.cif

Summary of feedback from opening
C:/Users/eliferd/Downloads/Choline_Oxidase_CO6_benchling.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for MET /A:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Choline_Oxidase_CO6_benchling.cif #2  
---  
Chain | Description  
A | No description available  
  

> mlp

Map values for surface "Choline_Oxidase_CO6_benchling.cif_A SES surface":
minimum -28.83, mean -5.37, maximum 24.51  
Map values for surface "Choline_Ox_WT_benchling.cif_A SES surface": minimum
-30.45, mean -5.326, maximum 24.81  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

> hide surfaces

> close session

> open "C:\Users\eliferd\OneDrive - Danmarks Tekniske
> Universitet\Skrivebord\Interfaces\Projects\Hydrophobins\17dew____.pdb"
> format pdb

Chain information for 17dew____.pdb #1  
---  
Chain | Description  
? | No description available  
  

> close session

> open C:\Users\eliferd\Downloads\Choline_Oxidase_CO6_benchling.cif format
> mmcif

Summary of feedback from opening
C:\Users\eliferd\Downloads\Choline_Oxidase_CO6_benchling.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for MET /A:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Choline_Oxidase_CO6_benchling.cif #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Model Loops"

> ui tool show "Surface Zone"


===== 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: 3.3.0 - Build 27.20.100.8853
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteBook 840 G7 Notebook PC
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 16,942,211,072
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
OSLanguage: en-US
Locale: ('da_DK', 'cp1252')
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-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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    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
    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
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1