Opened 5 years ago

Closed 5 years ago

#4609 closed defect (duplicate)

Problem fetching Modeller scores

Reported by: swamy02_vet@… 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:        Linux-5.8.0-50-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/swamy/folder_d/TLR3/modeller_dimer/HKCT3D/chimerax/dimer/success/alignment/3ciyA_t3dim.pir

Summary of feedback from opening
/home/swamy/folder_d/TLR3/modeller_dimer/HKCT3D/chimerax/dimer/success/alignment/3ciyA_t3dim.pir  
---  
notes | Alignment identifier is 3ciyA_t3dim.pir  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3ciyA_t3dim.pir  
  
Opened 2 sequences from 3ciyA_t3dim.pir  

> open 3ciy

3ciy title:  
Mouse Toll-like receptor 3 ectodomain complexed with double-stranded RNA [more
info...]  
  
Chain information for 3ciy #1  
---  
Chain | Description  
A B | Toll-like receptor 3  
C | 46-mer  
D | 46-mer  
  
Non-standard residues in 3ciy #1  
---  
BMA — beta-D-mannopyranose  
FUC — alpha-L-fucopyranose  
FUL — beta-L-fucopyranose (6-deoxy-β-L-galactose)  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose  
  
Associated 3ciy chain A to 3ciy chain A,B with 0 mismatches  
Associated 3ciy chain B to 3ciy chain A,B with 0 mismatches  

> open
> /home/swamy/folder_d/TLR3/modeller_dimer/HKCT3D/chimerax/dimer/success/alignment/3ciyA_t3dim.pir

Summary of feedback from opening
/home/swamy/folder_d/TLR3/modeller_dimer/HKCT3D/chimerax/dimer/success/alignment/3ciyA_t3dim.pir  
---  
notes | Alignment identifier is 3ciyA_t3dim.pir  
Associated 3ciy chain A to 3ciy chain A,B with 0 mismatches  
Associated 3ciy chain B to 3ciy chain A,B with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3ciyA_t3dim.pir  
  
Opened 2 sequences from 3ciyA_t3dim.pir  

> sequence associate /B 3ciyA_t3dim.pir:1

Disassociated 3ciy chain B from 3ciy chain A,B  
Associated 3ciy chain B to HKCT3 chain A,B with 158 mismatches and/or gaps  

> ui tool show "Modeller Comparative"

No target sequence chosen for alignment 3ciyA_t3dim.pir  

> modeller comparative 3ciyA_t3dim.pir:1 multichain true numModels 5 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: appModeller9v8Service1620426845295728547354  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1620426845295728547354  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1620426845295728547354 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 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence
alignment score = 2672  
Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence
alignment score = 2682.2  
RMSD between 1002 pruned atom pairs is 0.941 angstroms; (across all 1329
pairs: 1.979)  
  
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 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence
alignment score = 2675  
Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence
alignment score = 2702.6  
RMSD between 1209 pruned atom pairs is 1.195 angstroms; (across all 1329
pairs: 1.310)  
  
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 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence
alignment score = 2682.8  
Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence
alignment score = 2696.6  
RMSD between 1061 pruned atom pairs is 1.002 angstroms; (across all 1329
pairs: 1.557)  
  
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 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence
alignment score = 2675  
Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence
alignment score = 2685.2  
RMSD between 739 pruned atom pairs is 0.848 angstroms; (across all 1329 pairs:
2.578)  
  
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 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence
alignment score = 2675  
Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence
alignment score = 2685.8  
RMSD between 714 pruned atom pairs is 0.756 angstroms; (across all 1329 pairs:
4.892)  
  
Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches  
Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches  
Chain information for HKCT3_chain_A,B  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.1/B 2.2/B 2.3/B 2.4/B 2.5/B | No description
available  
  

> modeller scores #2.1-5 refresh false

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/httpq.py", line 115, in run  
func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 173, in start  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py", line 1968, in
parseString  
return expatbuilder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 925,
in parseString  
return builder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/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 "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 223,
in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/httpq.py", line 115, in run  
func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 173, in start  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py", line 1968, in
parseString  
return expatbuilder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 925,
in parseString  
return builder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/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 "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 223,
in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/httpq.py", line 115, in run  
func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 173, in start  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py", line 1968, in
parseString  
return expatbuilder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 925,
in parseString  
return builder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/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 "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 223,
in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/httpq.py", line 115, in run  
func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 173, in start  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py", line 1968, in
parseString  
return expatbuilder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 925,
in parseString  
return builder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/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 "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 223,
in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/webservices/httpq.py", line 115, in run  
func(*args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 66, in __init__  
self.start(session, modeller_host, license_key, structure, refresh,
blocking=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 173, in start  
self.run(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/modeller/scores.py", line 87, in launch  
sub_dom = parseString(submission)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py", line 1968, in
parseString  
return expatbuilder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 925,
in parseString  
return builder.parseString(string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/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 "/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py", line 223,
in parseString  
parser.Parse(string, True)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 20.2.6
OpenGL renderer: Mesa Intel(R) HD Graphics 620 (KBL GT2)
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 15-3567
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz
Cache Size: 3072 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          7.6Gi       1.7Gi       3.9Gi       546Mi       2.0Gi       5.2Gi
	Swap:          14Gi          0B        14Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 620 [8086:5916] (rev 02)	
	DeviceName:  Onboard IGD	
	Subsystem: Dell HD Graphics 620 [1028:078b]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    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: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Problem fetching Modeller scores

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: accepted → closed

Hi,

Thanks for reporting this problem. It has been fixed and the fix is available in the current daily build and the 1.2.1 release candidate, so if you install one of those then things will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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