Opened 4 years ago

Closed 4 years ago

#4561 closed defect (fixed)

syntax error submitting Modeller scoring request

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202103170256 (2021-03-17 02:56:09 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.dev202103170256 (2021-03-17)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/tig_m/Documents/ThesisProject/LipidBound/ChimeraXModels/CaliforniaSeaLionApoA1/A0A6J2BWZ3.fasta

Summary of feedback from opening
C:/Users/tig_m/Documents/ThesisProject/LipidBound/ChimeraXModels/CaliforniaSeaLionApoA1/A0A6J2BWZ3.fasta  
---  
note | Alignment identifier is A0A6J2BWZ3.fasta  
  
Opened 1 sequences from A0A6J2BWZ3.fasta  

> blastprotein A0A6J2BWZ3.fasta:1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1619416011975-281269463  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1619416011975-281269463  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Alignment identifier is bp1 [1]  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]  

> open pdbe_bio:1AV1

Summary of feedback from opening 1AV1 fetched from pdbe_bio  
---  
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.  
  
1AV1 bioassembly 1 title:  
Crystal structure of human apolipoprotein A-I [more info...]  
  
Chain information for 1AV1 bioassembly 1 #1  
---  
Chain | Description  
A B C D | apolipoprotein A-I  
  
Associated 1AV1 bioassembly 1 chain A to 1AV1_A with 0 mismatches  
Associated 1AV1 bioassembly 1 chain B to 1AV1_A with 0 mismatches  
Associated 1AV1 bioassembly 1 chain C to 1AV1_A with 0 mismatches  
Associated 1AV1 bioassembly 1 chain D to 1AV1_A with 0 mismatches  
Opened 1 biological assemblies for 1AV1  

> delete /C-D

> ui tool show "Modeller Comparative"

> modeller comparative "bp1 [1]:1" multichain true numModels 10 fast false
> hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1619416067365971194287  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1619416067365971194287  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1619416067365971194287 finished  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 915.3  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 893.1  
RMSD between 191 pruned atom pairs is 1.206 angstroms; (across all 402 pairs:
4.419)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 917.7  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 896.1  
RMSD between 132 pruned atom pairs is 0.828 angstroms; (across all 402 pairs:
5.837)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 911.7  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 893.1  
RMSD between 104 pruned atom pairs is 0.844 angstroms; (across all 402 pairs:
10.925)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 917.7  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 889.5  
RMSD between 83 pruned atom pairs is 1.134 angstroms; (across all 402 pairs:
5.887)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 915.3  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 899.7  
RMSD between 110 pruned atom pairs is 0.962 angstroms; (across all 402 pairs:
7.538)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 915.3  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 893.1  
RMSD between 127 pruned atom pairs is 1.346 angstroms; (across all 402 pairs:
7.851)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 915.3  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 896.1  
RMSD between 109 pruned atom pairs is 1.254 angstroms; (across all 402 pairs:
4.882)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 915.3  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 889.5  
RMSD between 76 pruned atom pairs is 1.206 angstroms; (across all 402 pairs:
7.230)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 915.3  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 895.5  
RMSD between 213 pruned atom pairs is 1.101 angstroms; (across all 402 pairs:
5.029)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1AV1 bioassembly 1, chain A (#1) with query, chain A (#), sequence
alignment score = 915.3  
Matchmaker 1AV1 bioassembly 1, chain B (#1) with query, chain B (#), sequence
alignment score = 896.7  
RMSD between 213 pruned atom pairs is 1.082 angstroms; (across all 402 pairs:
5.915)  
  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Associated query chain A to query with 0 mismatches  
Associated query chain B to query with 0 mismatches  
Chain information for query  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.1/B 2.2/B 2.3/B
2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B | No description available  
  
Associated query (2.1) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.1) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.2) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.2) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.3) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.3) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.4) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.4) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.5) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.5) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.6) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.6) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.7) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.7) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.8) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.8) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.9) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.9) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.10) chain A to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  
Associated query (2.10) chain B to tr|A0A6J2BWZ3|A0A6J2BWZ3_ZALCA
apolipoprotein A-I OS=Zalophus californianus OX=9704 GN=APOA1 PE=3 SV=1 with 0
mismatches  

> modeller scores #2.1-10 refresh false

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\webservices\httpq.py", line 115, in run  
func(*args)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 173, in start  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202103170256\bin\lib\site-
packages\chimerax\modeller\scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\minidom.py", line 1969, in parseString  
return expatbuilder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 925, in parseString  
return builder.parseString(string)  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
Error generating/processing HTTP request:  
xml.parsers.expat.ExpatError: syntax error: line 1, column 49  
  
File "C:\Program Files\ChimeraX
1.2.dev202103170256\bin\lib\xml\dom\expatbuilder.py", line 223, in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8853
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20SL
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 16,868,241,408
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.11.2
    ChimeraX-AtomicLibrary: 2.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103170256
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    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
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.3
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.17
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → syntax error submitting Modeller scoring request

Reported by Tiglath Moradkhan

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Modeller scoring server moved to https

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