ViewDockX: No suitable models found for ViewDockX

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-08)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-12-08)  
How to cite UCSF ChimeraX  
  
  
BB2 WT.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) BB2-WT [more info...]  
  
Chain information for BB2 WT.pdb #1.1  
---  
Chain | Description  
A B C D | No description available  
  
W151R.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) W51R FL [more info...]  
  
Chain information for W151R.pdb #1.2  
---  
Chain | Description  
A B C D | No description available  
  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> close #1.2

> open /Users/james/Downloads/W51R_FL_2018-12-11/model/01/templates/W151R.pdb

W151R.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) W51R FL [more info...]  
  
Chain information for W151R.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> view clip false

> close #1.1

> close #1

> open "/Users/james/Downloads/W51R_FL_2018-12-11/model/01/templates/BB2
WT.pdb"

BB2 WT.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) BB2-WT [more info...]  
  
Chain information for BB2 WT.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> select #1

5880 atoms, 6048 bonds selected  

> select #2

5868 atoms, 6028 bonds selected  

> ~select #2

Nothing selected  

could not retrieve bundle list from toolshed  

Incomplete command: sequence  

> help help:credits.html

> toolshed show "Volume Viewer"

> ui mousemode rightMode translate selected models

> show selAtoms ribbons

> hbonds selAtoms

2832 hydrogen bonds found  

> hbonds selAtoms

2832 hydrogen bonds found  

> ui mousemode rightMode distance

> ui mousemode rightMode distance

> ui mousemode rightMode move planes

Incomplete command: sequence  

> select protein

11748 atoms, 12076 bonds, 2832 pseudobonds, 1 model selected  

> toolshed show "Blast Protein"

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  

> toolshed show "Model Panel"

Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service15445441971071044330093  
Opal status URL:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15445441971071044330093  
BlastProtein finished.  

> open pdb:1YTQ

Summary of feedback from opening 1YTQ fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ytq from
http://files.rcsb.org/download/1ytq.cif  
Fetching CCD LEU from http://ligand-expo.rcsb.org/reports/L/LEU/LEU.cif  
Fetching CCD ASN from http://ligand-expo.rcsb.org/reports/A/ASN/ASN.cif  
Fetching CCD PRO from http://ligand-expo.rcsb.org/reports/P/PRO/PRO.cif  
Fetching CCD LYS from http://ligand-expo.rcsb.org/reports/L/LYS/LYS.cif  
Fetching CCD ILE from http://ligand-expo.rcsb.org/reports/I/ILE/ILE.cif  
Fetching CCD PHE from http://ligand-expo.rcsb.org/reports/P/PHE/PHE.cif  
Fetching CCD GLU from http://ligand-expo.rcsb.org/reports/G/GLU/GLU.cif  
Fetching CCD GLN from http://ligand-expo.rcsb.org/reports/G/GLN/GLN.cif  
Fetching CCD GLY from http://ligand-expo.rcsb.org/reports/G/GLY/GLY.cif  
Fetching CCD HIS from http://ligand-expo.rcsb.org/reports/H/HIS/HIS.cif  
Fetching CCD SER from http://ligand-expo.rcsb.org/reports/S/SER/SER.cif  
Fetching CCD CYS from http://ligand-expo.rcsb.org/reports/C/CYS/CYS.cif  
Fetching CCD THR from http://ligand-expo.rcsb.org/reports/T/THR/THR.cif  
Fetching CCD VAL from http://ligand-expo.rcsb.org/reports/V/VAL/VAL.cif  
Fetching CCD ALA from http://ligand-expo.rcsb.org/reports/A/ALA/ALA.cif  
Fetching CCD TRP from http://ligand-expo.rcsb.org/reports/T/TRP/TRP.cif  
Fetching CCD TYR from http://ligand-expo.rcsb.org/reports/T/TYR/TYR.cif  
Fetching CCD ARG from http://ligand-expo.rcsb.org/reports/A/ARG/ARG.cif  
Fetching CCD ASP from http://ligand-expo.rcsb.org/reports/A/ASP/ASP.cif  
Fetching CCD MET from http://ligand-expo.rcsb.org/reports/M/MET/MET.cif  
Fetching CCD HOH from http://ligand-expo.rcsb.org/reports/H/HOH/HOH.cif  
  
1ytq title:  
Structure of Native Human β B2 Crystallin [more info...]  
  
Chain information for 1ytq #4  
---  
Chain | Description  
A | β crystallin B2  
  
1ytq mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  
  

> matchmaker #4/A to #1/A

Parameters  
---  
Chain pairing | bb  
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 BB2 WT.pdb, chain A (#1) with 1ytq, chain A (#4), sequence
alignment score = 935.2  
RMSD between 178 pruned atom pairs is 0.407 angstroms; (across all 181 pairs:
0.524)  
  

> hide #!4 models

> show #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> view #1 clip false

No displayed objects specified.  

No displayed objects specified.  

> view #4 clip false

> show #4 target m

> toolshed show "Basic Actions"

> hide #1/A target c

> toolshed show "Cage Builder"

> toolshed show "Command Line Interface"

> toolshed show Log

> toolshed show "Remote Control"

xmlrpc server running at 127.0.0.1 on port 42184  

> toolshed show "Side View"

> toolshed show ViewDockX

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 575, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1235, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/viewdockx/__init__.py", line 15, in start_tool  
tool.setup()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/viewdockx/tool.py", line 22, in setup  
self._setup(structures)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/viewdockx/tool.py", line 53, in _setup  
raise ValueError("No suitable models found for ViewDockX")  
ValueError: No suitable models found for ViewDockX  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 930, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 581, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ViewDockX
in bundle ChimeraX-ViewDockX:  
No suitable models found for ViewDockX  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ViewDockX
in bundle ChimeraX-ViewDockX:  
No suitable models found for ViewDockX  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 581, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.2.17
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

[Conrad Huang]

Fixed in ea93d0e.

Raise UserError instead of ValueError when no suitable models are found.