id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2672 Toolshed down j.r.lewandowski@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.91 (2019-12-10) Description Hi Tom, Thanks for implementing ISOLDE tugging in VR. This is going to be a really awesome feature. I think at the moment I am happy with the rotations being performed while ISOLDE is paused but it would indeed be great if there was solution for this that would work during ISOLDE simulation. However, when I replaced the isolde.py and tugging.py I get an error message, which you can find in the log. And then ISOLDE is not fully loading. I think I may have dev 6 of ISOLDE, instead of dev 8 that you have used for editing the files. I tried to update to dev 8 but I cannot connect to the toolshed page withing the ChimeraX browser because the certificate expired. I downloaded the whl file separately but I am not sure how to install it in ChimeraX from command line. I have uodated CHimeraX to the daily build. Hopefully, the error will disappear when I update to ISOLDE 1.0b3.dev8 but I thought I let you know in case the problem is not related to that. Thanks. Best, Józef Log: UCSF ChimeraX version: 0.91 (2019-12-10) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open d:\data\Projects\TycACOM\TycACOM-TycC1CK9D-ISOLDE.pdb format PDB Summary of feedback from opening d:\data\Projects\TycACOM\TycACOM- TycC1CK9D-ISOLDE.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME=""complex_5w.pdb0"" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_5.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 31 messages similar to the above omitted Chain information for TycACOM-TycC1CK9D-ISOLDE.pdb #1 --- Chain | Description A | No description available B | No description available > toolshed show ISOLDE > set selectionWidth 4 Traceback (most recent call last): File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 627, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1612, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\\__init__.py"", line 48, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File ""D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py"", line 214, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\tool.py"", line 168, in __init__ self.isolde = isolde.Isolde(self) File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\isolde.py"", line 253, in __init__ self._start_gui(gui) File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\isolde.py"", line 375, in _start_gui self._populate_menus_and_update_params() File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\isolde.py"", line 436, in _populate_menus_and_update_params from .tutorials import populate_tutorial_combo_box ModuleNotFoundError: No module named 'chimerax.isolde.tutorials' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 1315, in run(ses, ""toolshed show %s"" % StringArg.unparse(tool_name))) File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\toolshed.py"", line 339, in toolshed_show bi.start_tool(session, name) File ""D:\Program Files\ChimeraX\bin\lib\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: No module named 'chimerax.isolde.tutorials' chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: No module named 'chimerax.isolde.tutorials' File ""D:\Program Files\ChimeraX\bin\lib\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 418.91 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Tool Shed fixed chimera-programmers Tristan Croll all ChimeraX