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#3662 closed defect (fixed)

Re-install not reinstalling

Reported by:	Tristan Croll	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Tool Shed	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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 <module>  
from .rota_annotation import RotamerAnnotator  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/rota_annotation.py", line 17, in <module>  
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

Change History (5)

in reply to: 1 ; follow-up: 1 comment:1 by Tristan Croll, 5 years ago

If I increment the ISOLDE version number before rebuilding it gets me 
past this point. It would definitely be preferable to avoid this - 
having to increment it every time I want to test a slight change will 
get painful fast.

On 2020-08-28 13:00, ChimeraX wrote:

comment:2 by pett, 5 years ago

Component:	Unassigned → Tool Shed
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Re-install not reinstalling

comment:3 by Tristan Croll, 5 years ago

To be clear, this only seems to happen for bundles that have to restart ChimeraX in order to install. Rebuilding Clipper still works as before.

comment:4 by Greg Couch, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Should be fixed :-). Add code to rebuild installed bundle cache if there are pip actions on restart.

in reply to: 5 ; follow-up: 5 comment:5 by Tristan Croll, 5 years ago

Did it make it into today's build (details below)? If so, it's still not 
working. Same long hang on startup, and the installed code isn't 
updated. If I go to the install directory and grep for the offending 
line (a call to view.first_intercept() that should be replaced with 
view.picked_object()):

cd ~/.local/share/ChimeraX/1.1/site-packages/chimerax/isolde
cat tugging.py|grep first_intercept
             pick = v.first_intercept(x, y, self._pick_exclude)

... when in the code in my source tree that I built with "make 
app-install" the same line is:
             pick = v.picked_object(x, y, self._pick_exclude)


built: 2020-09-01 05:11:50 PDT
committed: 2020-08-31 13:18:51 PDT
size: 280.6 MiB
md5: e62bff4d2c310737fac811a744384a3d

On 2020-08-31 07:44, ChimeraX wrote:

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