Web services not starting

[tharikadilhari@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.5.dev202209281710 (2022-09-28 17:10:28 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202209281710 (2022-09-28)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5TTU

5ttu title:  
Jak3 with covalent inhibitor 7 [more info...]  
  
Chain information for 5ttu #1  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase JAK3 | JAK3_HUMAN  
  
Non-standard residues in 5ttu #1  
---  
7KV —
1-[(3aR,7aR)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)octahydro-6H-pyrrolo[2,3-c]pyridin-6-yl]propan-1-one  
SO4 — sulfate ion  
  

> select coil

569 atoms, 565 bonds, 2 pseudobonds, 76 residues, 2 models selected  

> color (#!1 & sel) yellow

> select helix

1167 atoms, 1185 bonds, 144 residues, 1 model selected  

> color sel cornflower blue

> select strand

407 atoms, 402 bonds, 51 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel peach puff

> select ::name="7KV"

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

> color sel lime

> select ::name="7KV"

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

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:830

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

> select /A:830-834

13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected  

> ui tool show "Model Loops"

> modeller refine 1/A:1:27-31 numModels 5 fast false adjacentFlexible 1
> protocol DOPE-HR

Webservices job id: QZYXYLN1DYUWZS5X  

> ui tool show "Model Panel"

> select /A:829-830

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:829-835

23 atoms, 21 bonds, 1 pseudobond, 4 residues, 2 models selected  

> select /A:830

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

> select /A:830-834

13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected  

> color (#!1 & sel) red

> ui tool show "Model Loops"

> modeller refine 1/A:1:all-missing numModels 5 fast true adjacentFlexible 1
> protocol DOPE-HR

Webservices job id: XL1I781PTHGZ0RXE  

> ui tool show "Modeller Comparative"

> modeller comparative 1/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Webservices job id: 3JVZWGOE6NPTSQEV  

> select ::name="7KV"

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

> ui tool show H-Bonds

> hbonds sel intraMol false intraRes false reveal true

3 hydrogen bonds found  

> select clear

> transparency 50

> select ::name="7KV"

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

> ui tool show H-Bonds

> hbonds sel intraMol false intraRes false reveal true

3 hydrogen bonds found  

> select sequence LVAVKQLQHS

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select

2405 atoms, 2226 bonds, 6 pseudobonds, 504 residues, 3 models selected  

> surface hidePatches (#!1 & sel)

> ui tool show Distances

> select /A:826

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

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  

> select /A:877

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

> select /A:877

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

> select
> /A:818-820,861-877,909-943,951-953,990-1002,1006-1022,1025-1038,1045-1056,1067-1078,1081-1085,1087-1099

1167 atoms, 1185 bonds, 144 residues, 1 model selected  

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  

> select clear

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  
No distances to delete!  
Exactly two atoms must be selected!  

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  

> select /A:822-829,835-841,850-953,955-959,962-965,972-973,980-982,1003-1005

1050 atoms, 1059 bonds, 1 pseudobond, 130 residues, 2 models selected  

> select /A:822-829,835-841,850-953,955-959,962-965,972-973,980-982,1003-1005

1050 atoms, 1059 bonds, 1 pseudobond, 130 residues, 2 models selected  

> select /A:855

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

> select /A:855-1003

1142 atoms, 1164 bonds, 1 pseudobond, 143 residues, 2 models selected  

> select /A:855

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

> select /A:855-978

949 atoms, 963 bonds, 1 pseudobond, 118 residues, 2 models selected  

> select /A:855-856

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:855

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

> select /A:855-953

757 atoms, 768 bonds, 1 pseudobond, 93 residues, 2 models selected  

> select /A:855-953

757 atoms, 768 bonds, 1 pseudobond, 93 residues, 2 models selected  

> select /A:855

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

> select /A:855-978

949 atoms, 963 bonds, 1 pseudobond, 118 residues, 2 models selected  

> select /A:855

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

> select /A:855-1003

1142 atoms, 1164 bonds, 1 pseudobond, 143 residues, 2 models selected  

> select /A:855

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

> select /A:855-1003

1142 atoms, 1164 bonds, 1 pseudobond, 143 residues, 2 models selected  

> select /A:856-857

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

> select /A:856-888

270 atoms, 274 bonds, 33 residues, 1 model selected  

> select /A:863-864

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

> select /A:829-864

236 atoms, 237 bonds, 1 pseudobond, 33 residues, 2 models selected  

> select /A:855-879

203 atoms, 205 bonds, 25 residues, 1 model selected  

> select /A:855-1004

1153 atoms, 1176 bonds, 1 pseudobond, 144 residues, 2 models selected  

> select /A:855

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

> select /A:855-980

969 atoms, 984 bonds, 1 pseudobond, 120 residues, 2 models selected  

> view sel

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> ui tool show Distances

> select /A:855

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

> select /A:855-1053

1505 atoms, 1536 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select /A:855-856

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:857

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

> select /A:857-1058

1526 atoms, 1557 bonds, 2 pseudobonds, 191 residues, 2 models selected  

> select /A:857

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

> select /A:857-1099

1838 atoms, 1883 bonds, 2 pseudobonds, 232 residues, 2 models selected  

> select /A:857-1099

1838 atoms, 1883 bonds, 2 pseudobonds, 232 residues, 2 models selected  
Exactly two atoms must be selected!  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-1053

1505 atoms, 1536 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select /A:855

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

> select /A:855-879

203 atoms, 205 bonds, 25 residues, 1 model selected  

> select /A:855-879

203 atoms, 205 bonds, 25 residues, 1 model selected  

> select /A:855-879

203 atoms, 205 bonds, 25 residues, 1 model selected  

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  

> select /A:822-928,945-946,955-959,962-965,972-973,980-982,1003-1005

930 atoms, 937 bonds, 2 pseudobonds, 117 residues, 2 models selected  

> select /A:822-1028

1573 atoms, 1604 bonds, 2 pseudobonds, 198 residues, 2 models selected  

> select clear

> select /A:855

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

> select /A:855

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

> select /A:855

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

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select clear

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select clear

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select /A:855

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

> select /A:855

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

> select /A:855-1053

1505 atoms, 1536 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select clear

> select /A:855-1053

1505 atoms, 1536 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select clear

> select /A:855

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

> select /A:855

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

> select /A:855

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

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select clear

> select /A:855

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

> select /A:855

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

> select /A:855

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

> select /A:841,855

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A:841,855-1099

1868 atoms, 1913 bonds, 2 pseudobonds, 235 residues, 2 models selected  

> select clear

> select /A:841,855-1099

1868 atoms, 1913 bonds, 2 pseudobonds, 235 residues, 2 models selected  

> select clear

> select /A:855

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

> select /A:855

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

> select /A:841,855

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A:841-855

107 atoms, 108 bonds, 15 residues, 1 model selected  

> select /A:841-1053

1603 atoms, 1636 bonds, 2 pseudobonds, 202 residues, 2 models selected  

> select /A:843-844

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

> select /A:844-1030

1435 atoms, 1465 bonds, 1 pseudobond, 181 residues, 2 models selected  
Either three or four atoms must be selected!  

> select clear

> select /A:855

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

> select /A:855

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

> select /A:841,855

21 atoms, 20 bonds, 2 residues, 1 model selected  
Either three or four atoms must be selected!  

> select /A:886

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:886

12 atoms, 12 bonds, 1 residue, 1 model selected  
Either three or four atoms must be selected!  

> select /A:855

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

> select /A:855

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

> select /A:855

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

> select /A:855,886

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A:841,855,886

33 atoms, 32 bonds, 3 residues, 1 model selected  
Either three or four atoms must be selected!  

> save C:/Users/Dilshan/Desktop/ADRB_loop.pdb relModel #1

> cartoon hide sel

> select :828-

Expected an objects specifier or a keyword  

> 836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9

Unknown command:
836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9  

> 05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004

Unknown command:
05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004  

> select :828-

Expected an objects specifier or a keyword  

> 836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9

Unknown command:
836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9  

> 05:908:909:911:912:948:949:953:954:956:966-972:981:983-

Unknown command: 05:908:909:911:912:948:949:953:954:956:966-972:981:983-  

> 990:994:1004

Unknown command: 990:994:1004  

> select
> :828-836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9

167 atoms, 156 bonds, 1 pseudobond, 21 residues, 2 models selected  

> 05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004

Unknown command:
05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004  

> select:828-836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9

Unknown command:
select:828-836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9  

> 05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004

Unknown command:
05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004  

> select
> :828-836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:905:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004

379 atoms, 363 bonds, 1 pseudobond, 49 residues, 2 models selected  

> surface (#!1 & sel)

> select

2405 atoms, 2226 bonds, 6 pseudobonds, 504 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select ::name="7KV"

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

> select sel :< 5

175 atoms, 159 bonds, 3 pseudobonds, 30 residues, 2 models selected  

> select sel :< 4.5

2216 atoms, 511 bonds, 4 pseudobonds, 315 residues, 3 models selected  

> style sel stick

Changed 2216 atom styles  

> show sel atoms

> show sel surfaces

> ui tool show "Measure Volume and Area"

QWindowsWindow::setGeometry: Unable to set geometry 1366x726+0+23 (frame:
1382x765-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1366x705+0+23 (frame: 1382x744-8-8) margins: 8, 31, 8, 8
minimum size: 472x726 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=488, y=765)))  

> close session

Modeller job (ID 3JVZWGOE6NPTSQEV) finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 228, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 30 Sep 2022 18:59:57
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '70', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file stderr.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 661, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\modeller\common.py", line 563, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 18:59:57 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stderr.txt"}\'\n'  
  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 18:59:57 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stderr.txt"}\'\n'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
  
See log for complete Python traceback.  
  
Modeller job (ID QZYXYLN1DYUWZS5X) finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 228, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 30 Sep 2022 18:59:59
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '70', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file stderr.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 661, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\modeller\common.py", line 563, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 18:59:59 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stderr.txt"}\'\n'  
  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 18:59:59 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stderr.txt"}\'\n'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
  
See log for complete Python traceback.  
  
Modeller job (ID XL1I781PTHGZ0RXE) finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 228, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 30 Sep 2022 19:00:00
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '70', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file stderr.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 661, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\modeller\common.py", line 563, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 19:00:00 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stderr.txt"}\'\n'  
  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 19:00:00 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stderr.txt"}\'\n'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13399 Core Profile Forward-Compatible Context 15.201.1151.0
OpenGL renderer: AMD Radeon HD 6310 Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: TOSHIBA
Model: Satellite C855D
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 6,007,668,736
MaxProcessMemory: 137,438,953,344
CPU: 2 AMD E-300 APU with Radeon(tm) HD Graphics
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.3
    ChimeraX-AtomicLibrary: 8.0.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.2
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202209281710
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.0
    filelock: 3.7.1
    fonttools: 4.37.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.8.1