id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2174 Could not install ISOLDE/Clipper: EnvironmentError chimerax-bug-report@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.8 (2018-12-17) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\\\__init__.py"", line 338, in __init__ self.init_available_from_cache(logger) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\\\__init__.py"", line 445, in init_available_from_cache abc.load_from_cache() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\available.py"", line 61, in load_from_cache b = _build_bundle(d) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\available.py"", line 242, in _build_bundle keywords = _extract_extra_keywords(keywords) File ""C:\Program Files\ChimeraX\bin\lib\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 (2018-12-17) How to cite UCSF ChimeraX > open ""D:\SAMSON docking\HMG-reductase.pdb"" Summary of feedback from opening D:\SAMSON docking\HMG-reductase.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Accelrys Discovery Studio PDB file Ignored bad PDB record found on line 2 REMARK Created: 2019-07-04T20:22:41Z Chain information for HMG-reductase.pdb #1 --- Chain | Description A | No description available Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 386, in download_finished session=self.session) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 548, in install_bundle results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 845, in _pip_install results = self._run_pip(command) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 872, in _run_pip raise RuntimeError(s) RuntimeError: ERROR: Traceback (most recent call last): \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\\\__init__.py"", line 338, in __init__ \xa0\xa0\xa0\xa0self.init_available_from_cache(logger) \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\\\__init__.py"", line 445, in init_available_from_cache \xa0\xa0\xa0\xa0abc.load_from_cache() \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\available.py"", line 61, in load_from_cache \xa0\xa0\xa0\xa0b = _build_bundle(d) \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\available.py"", line 242, in _build_bundle \xa0\xa0\xa0\xa0keywords = _extract_extra_keywords(keywords) \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\installed.py"", line 270, in _extract_extra_keywords \xa0\xa0\xa0\xa0all_kwds = [k.strip() for k in kwds.split(',')] AttributeError: 'list' object has no attribute 'split' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\acer\downloads\chimerax_isolde-1.0b2-cp36-cp36m-win_amd64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b2) (0.8) Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2) Using cached https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3/ChimeraX_Clipper-0.3-cp36-cp36m-win_amd64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b2) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- Atomic>=0.7->ChimeraX-ISOLDE==1.0b2) (1.0) Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE Could not install packages due to an EnvironmentError: [WinError 5] Acc\xe8s refus\xe9: 'C:\\\Program Files\\\ChimeraX\\\bin\\\Lib\\\site- packages\\\chimerax\\\clipper' Consider using the `--user` option or check the permissions. You are using pip version 18.1, however version 19.1.1 is available. You should consider upgrading via the 'python -m pip install --upgrade pip' command. RuntimeError: ERROR: Traceback (most recent call last): \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\\\__init__.py"", line 338, in __init__ \xa0\xa0\xa0\xa0self.init_available_from_cache(logger) \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\\\__init__.py"", line 445, in init_available_from_cache \xa0\xa0\xa0\xa0abc.load_from_cache() \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\available.py"", line 61, in load_from_cache \xa0\xa0\xa0\xa0b = _build_bundle(d) \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\available.py"", line 242, in _build_bundle \xa0\xa0\xa0\xa0keywords = _extract_extra_keywords(keywords) \xa0\xa0File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\installed.py"", line 270, in _extract_extra_keywords \xa0\xa0\xa0\xa0all_kwds = [k.strip() for k in kwds.split(',')] AttributeError: 'list' object has no attribute 'split' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\acer\downloads\chimerax_isolde-1.0b2-cp36-cp36m-win_amd64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b2) (0.8) Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2) Using cached https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3/ChimeraX_Clipper-0.3-cp36-cp36m-win_amd64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b2) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- Atomic>=0.7->ChimeraX-ISOLDE==1.0b2) (1.0) Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE Could not install packages due to an EnvironmentError: [WinError 5] Acc\xe8s refus\xe9: 'C:\\\Program Files\\\ChimeraX\\\bin\\\Lib\\\site- packages\\\chimerax\\\clipper' Consider using the `--user` option or check the permissions. You are using pip version 18.1, however version 19.1.1 is available. You should consider upgrading via the 'python -m pip install --upgrade pip' command. File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 872, in _run_pip raise RuntimeError(s) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 20.19.15.4390 OpenGL renderer: Intel(R) HD Graphics 520 OpenGL vendor: Intel }}} " defect closed normal Tool Shed 0.8 fixed Tristan Croll all ChimeraX