id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2113 User installed tools should take precedence over app-included tools goddard@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-06-25) Description It seems that tools installed for this user only do not take precedence over tools in the ChimeraX app. I installed the Segger tool using the ChimeraX ""devel install"" command with the default ""user true"" and it put it in ~/Library/Application Support/ChimeraX/0.91/site-packages/chimerax/segger but the system path has this location after the ChimeraX app site-packages. In order to allow a newer Segger to be installed from the toolshed and replace the ChimeraX built in version the user installed tools need to take precedence over the app installed tools. Here is what ChimeraX reports at the system path. import sys sys.path ['/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python37.zip', '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7', '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload', '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages', '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg', '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyOpenGL_accelerate-3.1.3b1-py3.7-macosx-10.14-x86_64.egg', '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/tables-3.4.4-py3.7-macosx-10.14-x86_64.egg', '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numexpr-2.6.9-py3.7-macosx-10.14-x86_64.egg', '/Users/goddard/Library/Application Support/ChimeraX/0.91/site-packages', '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/IPython/extensions'] Log: UCSF ChimeraX version: 0.91 (2019-06-25) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/goddard/ucsf/chimerax/src/bundles/segger/test.cxs format session Summary of feedback from opening /Users/goddard/ucsf/chimerax/src/bundles/segger/test.cxs --- note | Showing 1080.seg - 14 regions, 14 surfaces opened ChimeraX session > toolshed show sh /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Tool Shed fixed all ChimeraX