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#9254 closed defect (not a bug)

Modeller failure

Reported by:	maria.levkovets@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Infrastructure	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Faced this issue when I was trying to model missing loops. One year ago everything worked.  

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

> open 2qke

2qke title:  
Wild Type Crystal Structure of Full Length Circadian Clock Protein KaiB from
Thermosynechococcus elongatus BP-1 [more info...]  
  
Chain information for 2qke #1  
---  
Chain | Description | UniProt  
A B C D E F | Circadian clock protein kaiB | KAIB_SYNEL  
  
2qke mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
4| software_defined_assembly  
5| software_defined_assembly  
  

> preset cartoons/nucleotides ribbons/slabs

Changed 4805 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> close session

> open 1kzg

Summary of feedback from opening 1kzg fetched from pdb  
---  
note | Fetching compressed mmCIF 1kzg from
http://files.rcsb.org/download/1kzg.cif  
  
1kzg title:  
DbsCdc42(Y889F) [more info...]  
  
Chain information for 1kzg #1  
---  
Chain | Description | UniProt  
A C | guanine nucleotide exchange factor DBS | MCF2L_MOUSE  
B D | CDC42 homolog | CDC42_HUMAN  
  
1kzg mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> select /A

2790 atoms, 2804 bonds, 1 pseudobond, 376 residues, 2 models selected  

> delete sel

> close session

> open 2kzg

2kzg title:  
A Transient and Low Populated Protein Folding Intermediate at Atomic
Resolution [more info...]  
  
Chain information for 2kzg  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Pre-mRNA-
processing factor 40 homolog A | PR40A_HUMAN  
  

> select #29-35

Nothing selected  

> select #29-35

Nothing selected  

> select #1.2-end

8433 atoms, 8514 bonds, 504 residues, 9 models selected  

> delete selected

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete sel

> select :29-35

100 atoms, 100 bonds, 7 residues, 1 model selected  

> delete sel

> ui tool show "Model Loops"

No alignments chosen for modeling  
[Repeated 1 time(s)]

> ui tool show "Model Loops"

> help help:user/tools/modelloops.html

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1.1/A  

> modeller refine 1.1/A:1:all-missing numModels 5 fast false adjacentFlexible
> 1 protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1346, in
do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1257, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1303, in
_send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1252, in
endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1012, in
_send_output  
self.send(msg)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 952, in send  
self.connect()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 923, in
connect  
self.sock = self._create_connection(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 822, in
create_connection  
for res in getaddrinfo(host, port, 0, SOCK_STREAM):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 953, in
getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
socket.gaierror: [Errno 11001] getaddrinfo failed  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 517, in
open  
response = self._open(req, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 534, in
_open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1375, in
http_open  
return self.do_open(http.client.HTTPConnection, req)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1349, in
do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [Errno 11001] getaddrinfo failed>  
  
Exception in thread 1:  
urllib.error.URLError:  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1349, in
do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> ui tool show "Model Loops"

> select /A:24

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:24-27

75 atoms, 74 bonds, 4 residues, 1 model selected  

> select /A:28

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select /A:36

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:36-38

56 atoms, 57 bonds, 3 residues, 1 model selected  

> select /A:38

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:38

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:13-46,49-54,58-63

663 atoms, 664 bonds, 1 pseudobond, 39 residues, 2 models selected  

> select /A:11-46

503 atoms, 506 bonds, 1 pseudobond, 29 residues, 2 models selected  

> select /A:11-54

634 atoms, 639 bonds, 1 pseudobond, 37 residues, 2 models selected  

> select /A:11-19

153 atoms, 154 bonds, 9 residues, 1 model selected  

> select /A:36-66

520 atoms, 525 bonds, 31 residues, 1 model selected  

> ui tool show "Model Loops"

> modeller refine 1.1/A:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1346, in
do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1257, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1303, in
_send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1252, in
endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1012, in
_send_output  
self.send(msg)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 952, in send  
self.connect()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 923, in
connect  
self.sock = self._create_connection(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 822, in
create_connection  
for res in getaddrinfo(host, port, 0, SOCK_STREAM):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 953, in
getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
socket.gaierror: [Errno 11001] getaddrinfo failed  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 517, in
open  
response = self._open(req, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 534, in
_open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1375, in
http_open  
return self.do_open(http.client.HTTPConnection, req)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1349, in
do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [Errno 11001] getaddrinfo failed>  
  
Exception in thread 2:  
urllib.error.URLError:  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1349, in
do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> select :56

11 atoms, 10 bonds, 1 residue, 1 model selected  

> вуд ыуд

Unknown command: вуд ыуд  

> delete sel

> ui tool show "Model Loops"

No alignments chosen for modeling  

> modeller refine 1.1/A:1:all-missing numModels 5 fast false adjacentFlexible
> 1 protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1346, in
do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1257, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1303, in
_send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1252, in
endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 1012, in
_send_output  
self.send(msg)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 952, in send  
self.connect()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\http\client.py", line 923, in
connect  
self.sock = self._create_connection(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 822, in
create_connection  
for res in getaddrinfo(host, port, 0, SOCK_STREAM):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\socket.py", line 953, in
getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
socket.gaierror: [Errno 11001] getaddrinfo failed  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 517, in
open  
response = self._open(req, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 534, in
_open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1375, in
http_open  
return self.do_open(http.client.HTTPConnection, req)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1349, in
do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [Errno 11001] getaddrinfo failed>  
  
Exception in thread 3:  
urllib.error.URLError:  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 1349, in
do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> select :51

10 atoms, 9 bonds, 1 residue, 1 model selected  

> вуд ыуд

Unknown command: вуд ыуд  

> delete sel

> ui tool show "Model Loops"

> modeller refine 1.1/A:1:all-missing numModels 5 fast false adjacentFlexible
> 1 protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 555, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 747, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 561, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 641, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 4:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> close session

> open 3v55

3v55 title:  
Human MALT1 (334-719) in its ligand free form [more info...]  
  
Chain information for 3v55 #1  
---  
Chain | Description | UniProt  
A | Mucosa-associated lymphoid tissue lymphoma translocation protein 1 |
MALT1_HUMAN  
  

> ui tool show "Model Loops"

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> modeller refine 1/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 555, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 747, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 561, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 641, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 5:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> ui tool show "Model Loops"

> modeller refine 1/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 555, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 747, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 561, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 641, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 6:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> ui tool show "Model Loops"

> modeller refine 1/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 555, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 747, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 561, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 641, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 7:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> ui tool show "Model Loops"

> help help:user/tools/modelloops.html

> modeller refine 1/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 555, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 747, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 561, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 641, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 8:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> select
> /A:361-376,387-401,435-439,442-450,510-517,524-539,573-583,636-640,642-646,651-655,659-663,674-678,710-715

889 atoms, 888 bonds, 111 residues, 1 model selected  

> select /A:542-546

38 atoms, 37 bonds, 5 residues, 1 model selected  

> select /A:542-670

1011 atoms, 1032 bonds, 129 residues, 1 model selected  

> select /A:672

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:672-712

326 atoms, 330 bonds, 41 residues, 1 model selected  

> select /A:717

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:717-719

29 atoms, 29 bonds, 3 residues, 1 model selected  

> select /A:337-380

359 atoms, 365 bonds, 44 residues, 1 model selected  

> select /A:405

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:405-423

148 atoms, 153 bonds, 19 residues, 1 model selected  

> select /A:445

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:426-445

154 atoms, 157 bonds, 20 residues, 1 model selected  

> select /A:407-408

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:407-502

648 atoms, 660 bonds, 2 pseudobonds, 81 residues, 2 models selected  

> select /A:405

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:405-411

55 atoms, 56 bonds, 7 residues, 1 model selected  

> select /A:482

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:482-492

81 atoms, 82 bonds, 11 residues, 1 model selected  

> select /A:498-505

62 atoms, 63 bonds, 8 residues, 1 model selected  

> select /A:493

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:493-494

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:492

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:492-498

27 atoms, 25 bonds, 1 pseudobond, 4 residues, 2 models selected  

> ui tool show "Model Loops"

> modeller refine 1/A:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 555, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 747, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 561, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 641, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 9:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> model.loops()

Unknown command: model.loops()  

> ui tool show "Model Loops"

> modeller refine 1/A:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 555, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 747, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 523, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 632, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 561, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 494, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\urllib\request.py", line 641, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\tasks.py", line 284, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 10:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\modeller\common.py", line 488, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.14830 Core Profile Forward-Compatible Context 21.10.20 27.20.21020.3
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Acer
Model: Swift SF314-42
OS: Майкрософт Windows 10 Pro (Build 19044)
Memory: 7,916,019,712
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 4500U with Radeon Graphics         
OSLanguage: ru-RU
Locale: ('ru_RU', 'cp1251')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component:	Unassigned → Infrastructure
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Modeller failure

comment:2 by Eric Pettersen, 2 years ago

Resolution:	→ not a bug
Status:	accepted → closed

Hi Maria,

The web services architecture that ChimeraX uses has changed since the 1.3 release that you are using. You will need to get a current release of ChimeraX in order to use web services like Modeller from ChimeraX.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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