id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2764 ISOLDE not longer compatible with 0.9 madhan@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-redhat-7.7-Nitrogen ChimeraX Version: 0.9 (2019-06-06) Description Dear ISOLDE, I am just trying to install ISOLDE program embedded in my chimerax but it fails with this message. Please could help me out? Log: UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /lmb/home/madhan/.cache/ChimeraX/0.9/installers/ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in /net/nfs1/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0b3) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.9 in /net/nfs1/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0b3) (0.9) Requirement already satisfied, skipping upgrade: ChimeraX-Clipper>=0.9.4 in /lmb/home/madhan/.local/share/ChimeraX/0.9/site-packages (from ChimeraX- ISOLDE==1.0b3) (0.10.0) Installing collected packages: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0b3 Uninstalling ChimeraX-ISOLDE-1.0b3: Successfully uninstalled ChimeraX-ISOLDE-1.0b3 Successfully installed ChimeraX-ISOLDE-1.0b3 Lock 47273222118144 acquired on /lmb/home/madhan/.cache/ChimeraX/0.9/toolshed/bundle_info.cache.lock Lock 47273222118144 released on /lmb/home/madhan/.cache/ChimeraX/0.9/toolshed/bundle_info.cache.lock You are using pip version 19.0.3, however version 19.3.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. > toolshed show ISOLDE Traceback (most recent call last): File ""/public/chimerax_public/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 ""/public/chimerax_public/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 ""/lmb/home/madhan/.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 ""/public/chimerax_public/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 ""/lmb/home/madhan/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/tool.py"", line 167, in __init__ from . import isolde File ""/lmb/home/madhan/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 35, in from chimerax import clipper File ""/lmb/home/madhan/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/__init__.py"", line 26, in __version__ = _version() File ""/lmb/home/madhan/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/__init__.py"", line 24, in _version return pkg_resources.require('ChimeraX-Clipper')[0].version File ""/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site- packages/pkg_resources/__init__.py"", line 900, in require needed = self.resolve(parse_requirements(requirements)) File ""/public/chimerax_public/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 (/net/nfs1/public/chimerax_public/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 ""/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 1137, in run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name))) File ""/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2632, in run result = ci.function(session, **kw_args) File ""/public/chimerax_public/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 ""/public/chimerax_public/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 (/net/nfs1/public/chimerax_public/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 (/net/nfs1/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site- packages), Requirement.parse('ChimeraX-Core==0.91'), {'ChimeraX-Clipper'}) File ""/public/chimerax_public/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 418.56 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party 0.9 fixed Eric Pettersen Conrad Huang all ChimeraX