The following bug report has been submitted:
Platform: Linux-4.15.0-46-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.8 (2018-11-28)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__
self.init_available_from_cache(logger)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 445, in
init_available_from_cache
abc.load_from_cache()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache
b = _build_bundle(d)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle
keywords = _extract_extra_keywords(keywords)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/installed.py", line 270, in
_extract_extra_keywords
all_kwds = [k.strip() for k in kwds.split(',')]
AttributeError: 'list' object has no attribute 'split'
UCSF ChimeraX version: 0.8 (2018-11-28)
How to cite UCSF ChimeraX
> open
/home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.yob
Unrecognized file suffix '.yob'
Unrecognized file suffix '.yob'
> open
/home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.pdb
Summary of feedback from opening
/home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for tilipo33_model-1.pdb #1
---
Chain | Description
A | biogenic amine-binding protein
> ~select #1
Nothing selected
> select #1
2617 atoms, 2644 bonds selected
> ~select #1
Nothing selected
> hide selAtoms ribbons
> 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
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service15553544029431093310020
Opal status URL:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15553544029431093310020
BlastProtein finished.
> hide selAtoms ribbons
> show selAtoms
> show selAtoms ribbons
> hide selAtoms ribbons
> show selAtoms ribbons
> hide selAtoms
> show selAtoms
> lighting full
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> hide selAtoms ribbons
> ui mousemode rightMode rotate and select
> ui mousemode rightMode translate
> ui mousemode rightMode select
> ui mousemode rightMode clip
> ui mousemode rightMode distance
> ui mousemode rightMode tug
> ui mousemode rightMode minimize
> hide selAtoms ribbons
> hide selAtoms
> show selAtoms ribbons
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl
Successfully installed ChimeraX-Clipper-0.3.1 ChimeraX-ISOLDE-1.0b2
Installed ChimeraX-Clipper (0.3.1)
Installed ChimeraX-ISOLDE (1.0b2)
Downloading bundle ChimeraX_Cytoscape-0.1-py3-none-any.whl
Successfully installed ChimeraX-Cytoscape-0.1
Installed ChimeraX-Cytoscape (0.1)
Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl
Successfully installed ChimeraX-Stringdb-0.1
Installed ChimeraX-Stringdb (0.1)
Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl
unloading module chimerax.stringdb
Successfully installed ChimeraX-Stringdb-0.1
Installed ChimeraX-Stringdb (0.1)
Downloading bundle ChimeraX_BlastProtein-0.1-py3-none-any.whl
unloading module chimerax.blastprotein
Successfully installed ChimeraX-BlastProtein-0.1
Installed ChimeraX-BlastProtein (0.1)
Downloading bundle ChimeraX_Tempy-0.6.0-py3-none-any.whl
unloading module chimerax.tempy
Successfully installed ChimeraX-Tempy-0.6.0
Installed ChimeraX-Tempy (0.6.0)
> toolshed show "Blast Protein"
> toolshed show "Density Map Toolbar"
> close session
> open "/media/ricardo/New
Volume/home/ricardo/aati/pedro_aati/AaTI/Refine_299/AaTI_Structure_refine_299.pdb"
Chain information for AaTI_Structure_refine_299.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open "/media/ricardo/New
Volume/home/ricardo/aati/pedro_aati/AaTI/Refine_299/AaTI_Structure_refine_data.mtz"
Must specify a structure model to associate with crystallographic data
Must specify a structure model to associate with crystallographic data
> volume selMaps style solid
No volumes specified
No volumes specified
> toolshed show Tempy
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1185, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/__init__.py", line 16, in start_tool
from .tool import ToolUI
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool.py", line 14, in <module>
from . import tool_scores
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool_scores.py", line 8, in <module>
from . import tool_select
File "/home/ricardo/.local/share/ChimeraX/0.8/site-
packages/chimerax/tempy/tool_select.py", line 8, in <module>
from chimerax.core.map.volume import Volume
ModuleNotFoundError: No module named 'chimerax.core.map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 922, in <lambda>
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show
bi.start_tool(session, tool_name)
File "/usr/lib/ucsf-chimerax-daily/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 Tempy in
bundle ChimeraX-Tempy:
No module named 'chimerax.core.map'
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Tempy in
bundle ChimeraX-Tempy:
No module named 'chimerax.core.map'
File "/usr/lib/ucsf-chimerax-daily/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.
> volume selMaps style mesh
No volumes specified
No volumes specified
> select #1
927 atoms, 844 bonds selected
> volume selMaps style solid
No volumes specified
No volumes specified
> ~select #1
Nothing selected
> toolshed show Registration
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 529, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/gui.py", line 67, in handle_scheme
self.session.ui.thread_safe(self._register, url)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 286, in thread_safe
func(*args, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/gui.py", line 121, in _register
join_announcements=values["join_announcements"])
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/cmd.py", line 76, in register
funding, funding_other, comment)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/cmd.py", line 120, in _get_registration
with urlopen(RegistrationURL, urlencode(params).encode()) as f:
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 223,
in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 532,
in open
response = meth(req, response)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 642,
in http_response
'http', request, response, code, msg, hdrs)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 570,
in error
return self._call_chain(*args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 504,
in _call_chain
result = func(*args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 650,
in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 500: Registration internal error
urllib.error.HTTPError: HTTP Error 500: Registration internal error
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py", line 650,
in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: Quadro K4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
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We broke Tempy when we moved
chimerax.core.maptochimerax.map. Not sure what to do about that.What data did you enter for registration (if any)? Looks like the server side bailed, but I need to reproduce it to fix it.