id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3662 Re-install not reinstalling Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.1rc202008252015 (2020-08-25 20:15:37 UTC) Description The ""install after restarting ChimeraX"" for bundles with a custom init doesn't seem to be working correctly. I was still importing from chimerax.core.geometry in a few places... did a global search-and-replace in the source tree and rebuilt with `make app-install`. ChimeraX hung for about a minute on startup (displayed the outline of the splash screen, but not the actual image). The log claims that it successfully installed the new wheel, but the traceback says it's still using the old code. I've double-checked inside the wheel file - it's definitely the updated code in there. Log: UCSF ChimeraX version: 1.1rc202008252015 (2020-08-25) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0.2-cp37-cp37m-linux_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /home/tic20/.cache/ChimeraX/1.1/installers/ChimeraX_ISOLDE-1.0.2-cp37-cp37m-linux_x86_64.whl Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-Clipper~=0.15.0 in /home/tic20/.local/share/ChimeraX/1.1/site-packages (from ChimeraX- ISOLDE==1.0.2) (0.15.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.2) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-UI~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.2) Requirement already satisfied: ChimeraX-Surface~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- ConnectStructure~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.1) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.1) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.1) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Map~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (1.0.1) Requirement already satisfied: ChimeraX-MapData~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.1) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (1.0.4) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-IO~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- SaveCommand~=1.0->ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-IO~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- SaveCommand~=1.0->ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.2) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.1) Requirement already satisfied: ChimeraX-IO~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- SaveCommand~=1.0->ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-UI~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.2) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2) Requirement already satisfied: ChimeraX-MapData~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.1) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- PDB~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.2) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Map~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (1.0.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-MapData~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Map~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (1.0.1) Requirement already satisfied: ChimeraX-UI~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.2.2) Requirement already satisfied: ChimeraX-MapData~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Map~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (1.0.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.1) Requirement already satisfied: ChimeraX-MapData~=2.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.6.0->ChimeraX- ISOLDE==1.0.2) (2.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Atomic~=1.6.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.6.1) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic~=1.6.0->ChimeraX-ISOLDE==1.0.2) (1.0) Requirement already satisfied: ChimeraX-Core~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0.2) (1.1rc202008252015) Lock 140012373022864 acquired on /home/tic20/.cache/ChimeraX/1.1/toolshed/bundle_info.cache.lock Lock 140012373022864 released on /home/tic20/.cache/ChimeraX/1.1/toolshed/bundle_info.cache.lock > open working.cxs Unable to restore session, resetting. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 669, in restore cls = name.class_of(self) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/session.py"", line 193, in class_of cls = bundle_info.get_class(class_name, session.logger) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 438, in get_class return f(class_name) File ""/home/tic20/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/__init__.py"", line 56, in get_class from .validation import RamaAnnotator, RotamerAnnotator File ""/home/tic20/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/__init__.py"", line 12, in from .rota_annotation import RotamerAnnotator File ""/home/tic20/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 17, in from chimerax.core.geometry import translation, rotation, Places ModuleNotFoundError: No module named 'chimerax.core.geometry' opened ChimeraX session OpenGL version: 3.3.0 NVIDIA 450.51.05 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 5.9G 38G 156M 18G 56G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1rc202008252015 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.0.2 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-Phenix: 0.1 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.2 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.6 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 4.3.3 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Tool Shed fixed all ChimeraX