Wrong version of Clipper (duplicate of #2214)

[JMHolton@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.4.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.9 (2019-06-06)
Description
Launching ISOLDE

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/validation/validation.py", line 165, in
generate_interpolator_data  
infile = open(os.path.join(cache_dir, file_prefix+'.pickle'), 'r+b')  
FileNotFoundError: [Errno 2] No such file or directory:
'/home/jamesh/.local/share/ChimeraX/0.9/isolde_data/rota8000-val.pickle'  
  
During handling of the above exception, another exception occurred:  
  
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 "/opt/UCSF/ChimeraX/lib/python3.7/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/isolde/tool.py",
line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 320, in __init__  
self._start_gui(gui)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 457, in _start_gui  
self._populate_menus_and_update_params()  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 556, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1011, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2412, in _change_selected_model  
self._update_iffy_rota_list()  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2330, in _update_iffy_rota_list  
rota_m = get_rotamer_mgr(self.session)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/session_extensions.py", line 63, in get_rotamer_mgr  
return Rota_Mgr(session)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 1151, in __init__  
self._prepare_all_validators()  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 1338, in _prepare_all_validators  
idata = validation.generate_interpolator_data(data_dir, cache_dir, fname,
True)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/validation/validation.py", line 175, in
generate_interpolator_data  
infile = open(full_path, 'r+t')  
PermissionError: [Errno 13] Permission denied:
'/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/validation/molprobity_data/rota8000-val.data'  
  
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:  
[Errno 13] Permission denied: '/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/validation/molprobity_data/rota8000-val.data'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
[Errno 13] Permission denied: '/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/isolde/validation/molprobity_data/rota8000-val.data'  
  
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 418.87.01
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

Hi James,

This is due to a long-standing bug affecting the ChimeraX 0.9 release, causing it to install a much more recent and incompatible version of Clipper when installing ISOLDE. I'd very strongly recommend installing the latest ChimeraX daily build and installing ISOLDE into that to get then most recent dev version - ChimeraX 0.9/ISOLDE 1.0b3 are almost 6 months old now, and a *lot* has changed since then.

I'll actually be putting up new builds today or tomorrow - probably best to hold out until they're up.

Best regards,

Tristan

[Tristan Croll]

Duplicate of #2214.