id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3710 Problem installing ISOLDE into 1.0 yonca.ural-blimke@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-19.6.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hi, I wanted to instal ISOLDE but get an error in the process Shortly: I clicked on the Tools/More Tools... (toolshed) tab and selected ISOLDE install. In the Log panel of chimeraX the following error appeared (posted below) and the installation was not successful (I could not find ISEOLDE in Tools/General/). I have MacOS, version 10.15.6 and installed chimeraX, version 1.0 from 2020-06-04. How can I instal and run ISOLDE from ChimeraX? Many Thanks, Yonca -- Log: Downloading bundle ChimeraX_ISOLDE-1.0.1-cp37-cp37m-macosx_10_13_x86_64.whl: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 193, in _run_module_as_main ""__main__"", mod_spec) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 85, in _run_code exec(code, run_globals) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/ChimeraX_main.py"", line 895, in exit_code = init(sys.argv) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/ChimeraX_main.py"", line 693, in init run_name='__main__', alter_sys=True) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 205, in run_module return _run_module_code(code, init_globals, run_name, mod_spec) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 85, in _run_code exec(code, run_globals) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pip/__main__.py"", line 10, in if sys.path[0] in ('', os.getcwd()): FileNotFoundError: [Errno 2] No such file or directory Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show Downloading bundle ChimeraX_ISOLDE-1.0.1-cp37-cp37m-macosx_10_13_x86_64.whl ERROR: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 193, in _run_module_as_main ""__main__"", mod_spec) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 85, in _run_code exec(code, run_globals) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/ChimeraX_main.py"", line 895, in exit_code = init(sys.argv) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/ChimeraX_main.py"", line 693, in init run_name='__main__', alter_sys=True) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 205, in run_module return _run_module_code(code, init_globals, run_name, mod_spec) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 85, in _run_code exec(code, run_globals) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pip/__main__.py"", line 10, in if sys.path[0] in ('', os.getcwd()): FileNotFoundError: [Errno 2] No such file or directory > toolshed show Downloading bundle ChimeraX_ISOLDE-1.0.1-cp37-cp37m-macosx_10_13_x86_64.whl ERROR: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 193, in _run_module_as_main ""__main__"", mod_spec) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 85, in _run_code exec(code, run_globals) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/ChimeraX_main.py"", line 895, in exit_code = init(sys.argv) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/ChimeraX_main.py"", line 693, in init run_name='__main__', alter_sys=True) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 205, in run_module return _run_module_code(code, init_globals, run_name, mod_spec) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 85, in _run_code exec(code, run_globals) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pip/__main__.py"", line 10, in if sys.path[0] in ('', os.getcwd()): FileNotFoundError: [Errno 2] No such file or directory > ui tool show Toolbar > toolshed show Downloading bundle ChimeraX_Clipper-0.14.0-cp37-cp37m-macosx_10_13_x86_64.whl ERROR: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 193, in _run_module_as_main ""__main__"", mod_spec) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 85, in _run_code exec(code, run_globals) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/ChimeraX_main.py"", line 895, in exit_code = init(sys.argv) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/ChimeraX_main.py"", line 693, in init run_name='__main__', alter_sys=True) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 205, in run_module return _run_module_code(code, init_globals, run_name, mod_spec) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py"", line 85, in _run_code exec(code, run_globals) File ""/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/pip/__main__.py"", line 10, in if sys.path[0] in ('', os.getcwd()): FileNotFoundError: [Errno 2] No such file or directory > help help:contact.html > toolshed show OpenGL version: 4.1 INTEL-14.7.8 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0) Software: System Software Overview: System Version: macOS 10.15.6 (19G2021) Kernel Version: Darwin 19.6.0 Time since boot: 2:51 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL U2715H: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 59 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: GH85D62F00FL Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: Thunderbolt/DisplayPort PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect assigned normal Tool Shed Tristan Croll all ChimeraX