Wrong version of ChimeraX for ISOLDE

[john.heumann@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-redhat-7.7-Maipo
ChimeraX Version: 0.9 (2019-06-06)
Description
Installing and starting Isolode from the production 0.9 release gives a tool start up error. (I'm using the production release since the 0.92 daily says Isolde is not yet avaiable.  Tool seems to be running despite the error. This is on RHEL7.7.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl  
Successfully installed ChimeraX-ISOLDE-1.0b3  
Installed ChimeraX-ISOLDE (1.0b3)  

'clip' is a prefix of an existing command 'clipper'  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1435, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/heumannj/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/__init__.py", line 31, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/tools.py",
line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/home/heumannj/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/tool.py", line 167, in __init__  
from . import isolde  
File "/home/heumannj/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 35, in <module>  
from chimerax import clipper  
File "/home/heumannj/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/__init__.py", line 26, in <module>  
__version__ = _version()  
File "/home/heumannj/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/__init__.py", line 24, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 900, in require  
needed = self.resolve(parse_requirements(requirements))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 791, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 0.9
(/opt/UCSF/ChimeraX/lib/python3.7/site-packages), Requirement.parse('ChimeraX-
Core==0.91'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line
1137, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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 ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9 (/opt/UCSF/ChimeraX/lib/python3.7/site-packages),
Requirement.parse('ChimeraX-Core==0.91'), {'ChimeraX-Clipper'})  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9 (/opt/UCSF/ChimeraX/lib/python3.7/site-packages),
Requirement.parse('ChimeraX-Core==0.91'), {'ChimeraX-Clipper'})  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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: 3.3.0 NVIDIA 440.44
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

Hi John,

For the latest ISOLDE version, you'll need the 0.91 candidate release build: ​http://preview.cgl.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=centos-7/ucsf-chimerax-0.91-1.el7.x86_64.rpm. Dev builds compatible with ChimeraX 0.92 will be coming in the next few weeks.

Hope you find it useful!

Tristan

[john.heumann@…]

Thanks, Tristan! I can easily wait for the 0.92 build next week.

Regards,
-jh-

On 1/7/20 2:06 AM, ChimeraX wrote: