ESMFold: name 'SearchError' is not defined

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The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6rc202303310103 (2023-03-31 01:03:33 UTC)
Description
(Describe the actions that caused this problem to occur here)NameError: name 'SearchError' is not defined File "D:\applications\ChimeraX\bin\lib\site-packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s' % url) See log for complete Python traceback. 

Log:
UCSF ChimeraX version: 1.6rc202303310103 (2023-03-31)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show ESMFold

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> ui tool show AlphaFold

> alphafold match Q62108

1 AlphaFold model found using UniProt identifier: Q62108 (UniProt Q62108)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
Q62108 | Q62108 | 100.0 | 100.0  
Opened 1 AlphaFold model  

> ui tool show ESMFold

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  

> esmfold match Q62108

Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 700, in urlopen  
self._prepare_proxy(conn)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 996, in _prepare_proxy  
conn.connect()  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 369, in connect  
self.sock = conn = self._connect_tls_proxy(hostname, conn)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\connection.py",
line 504, in _connect_tls_proxy  
socket = ssl_wrap_socket(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 453, in ssl_wrap_socket  
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\ssl_.py",
line 495, in _ssl_wrap_socket_impl  
return ssl_context.wrap_socket(sock)  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 500, in wrap_socket  
return self.sslsocket_class._create(  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1040, in _create  
self.do_handshake()  
File "D:\applications\ChimeraX\bin\lib\ssl.py", line 1309, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1129)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 489, in send  
resp = conn.urlopen(  
File "D:\applications\ChimeraX\bin\lib\site-
packages\urllib3\connectionpool.py", line 787, in urlopen  
retries = retries.increment(  
File "D:\applications\ChimeraX\bin\lib\site-packages\urllib3\util\retry.py",
line 592, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='www.rbvi.ucsf.edu', port=443): Max retries exceeded
with url: /chimerax/cgi-bin/esmfold_search_cgi.py (Caused by
SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol
(_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 47, in _search_sequences_web  
r = requests.post(url, data=request)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
115, in post  
return request("post", url, data=data, json=json, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\api.py", line
59, in request  
return session.request(method=method, url=url, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 587, in request  
resp = self.send(prep, **send_kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\sessions.py",
line 701, in send  
r = adapter.send(request, **kwargs)  
File "D:\applications\ChimeraX\bin\lib\site-packages\requests\adapters.py",
line 563, in send  
raise SSLError(e, request=request)  
requests.exceptions.SSLError: HTTPSConnectionPool(host='www.rbvi.ucsf.edu',
port=443): Max retries exceeded with url: /chimerax/cgi-
bin/esmfold_search_cgi.py (Caused by SSLError(SSLEOFError(8, 'EOF occurred in
violation of protocol (_ssl.c:1129)')))  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
NameError: name 'SearchError' is not defined  
  
NameError: name 'SearchError' is not defined  
  
File "D:\applications\ChimeraX\bin\lib\site-
packages\chimerax\esmfold\search.py", line 49, in _search_sequences_web  
raise SearchError('Unable to reach ESMFold sequence search web service\n\n%s'
% url)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 528.52
OpenGL renderer: NVIDIA GeForce RTX 4080 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 82WQ
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 34,158,272,512
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202303310103
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.1.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.2.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[Eric Pettersen]

Reported by Gu

[Tom Goddard]

Fixed.

ChimeraX was trying to search the ESMFold database for a specified uniprot sequence but it could not reach the UCSF web service that does the search. Probably our server was temporarily down. But the ChimeraX code that tried to report that error had a bug, missing SearchError class, so it didn't give a clear error message. I have fixed that bug in the ChimeraX 1.6 release candidate and daily build.

Thanks for reporting the problem!