Opened 3 years ago
Last modified 3 years ago
#7090 assigned defect
Toolbar buttons not created when ISOLDE installed
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tristan Croll, chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /Users/sconnell/Downloads
Current working directory is: /Users/sconnell/Downloads
> devel install ChimeraX_Clipper-0.18.0-cp39-cp39-macosx_10_13_x86_64.whl
Bundle info file
'ChimeraX_Clipper-0.18.0-cp39-cp39-macosx_10_13_x86_64.whl/bundle_info.xml' is
missing
> toolshed show
> toolshed install ChimeraX_Clipper-0.18.0-cp39-cp39-macosx_10_13_x86_64.whl
Errors may have occurred when running pip:
pip standard error:
\---
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages
sysconfig: /Users/sconnell/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages
sysconfig: /Users/sconnell/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-Clipper
sysconfig: /Users/sconnell/Library/Python/3.9/include/ChimeraX-Clipper
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application Support/ChimeraX/bin
sysconfig: /Users/sconnell/Library/Python/3.9/bin
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application Support/ChimeraX
sysconfig: /Users/sconnell/Library/Python/3.9
WARNING: Additional context:
user = True
home = None
root = None
prefix = None
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN
sysconfig: /Users/sconnell/Library/Python/3.9/include/UNKNOWN
WARNING: You are using pip version 21.3.1; however, version 22.1.2 is
available.
You should consider upgrading via the
'/Applications/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./ChimeraX_Clipper-0.18.0-cp39-cp39-macosx_10_13_x86_64.whl
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clipper==0.18.0) (1.0)
Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clipper==0.18.0) (7.0)
Requirement already satisfied: ChimeraX-Core~=1.4.dev202203030220 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clipper==0.18.0) (1.4)
Requirement already satisfied: ChimeraX-Atomic~=1.36 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clipper==0.18.0) (1.39.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.7)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0.2)
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.6.6)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.2)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0.2)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.2.2)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.5.1)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.9)
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.18.3)
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.0)
Requirement already satisfied: ChimeraX-IO~=1.0.1 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.0.1)
Requirement already satisfied: ChimeraX-Map~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1)
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.8)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.1)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)
Installing collected packages: ChimeraX-Clipper
Successfully installed ChimeraX-Clipper-0.18.0
\---
Successfully installed ChimeraX-Clipper-0.18.0
Installed ChimeraX-Clipper (0.18.0)
> toolshed install ChimeraX_ISOLDE-1.4b1-cp39-cp39-macosx_10_13_x86_64.whl
Errors may have occurred when running pip:
pip standard error:
\---
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages
sysconfig: /Users/sconnell/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages
sysconfig: /Users/sconnell/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-ISOLDE
sysconfig: /Users/sconnell/Library/Python/3.9/include/ChimeraX-ISOLDE
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application Support/ChimeraX/bin
sysconfig: /Users/sconnell/Library/Python/3.9/bin
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application Support/ChimeraX
sysconfig: /Users/sconnell/Library/Python/3.9
WARNING: Additional context:
user = True
home = None
root = None
prefix = None
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /Users/sconnell/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN
sysconfig: /Users/sconnell/Library/Python/3.9/include/UNKNOWN
WARNING: You are using pip version 21.3.1; however, version 22.1.2 is
available.
You should consider upgrading via the
'/Applications/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./ChimeraX_ISOLDE-1.4b1-cp39-cp39-macosx_10_13_x86_64.whl
Requirement already satisfied: ChimeraX-Clipper~=0.18.0 in
/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-packages (from
ChimeraX-ISOLDE==1.4b1) (0.18.0)
Requirement already satisfied: ChimeraX-Core~=1.4.dev202203030220 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.4b1) (1.4)
Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.4b1) (7.0)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.4b1) (1.0)
Requirement already satisfied: ChimeraX-Atomic~=1.36 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.4b1) (1.39.1)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.2)
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.6.6)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.0.2)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.7)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0.2)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.4b1) (1.2.2)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.4b1) (1.5.1)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.4b1) (1.9)
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.4b1) (1.0)
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.4b1) (1.18.3)
Requirement already satisfied: ChimeraX-IO~=1.0.1 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.4b1) (1.0.1)
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0)
Requirement already satisfied: ChimeraX-Map~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.1)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.8)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.0)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.1)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.1)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.0)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0)
Installing collected packages: ChimeraX-ISOLDE
Successfully installed ChimeraX-ISOLDE-1.4b1
\---
Successfully installed ChimeraX-ISOLDE-1.4b1
Installed ChimeraX-ISOLDE (1.4b1)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 127, in _set_button_starting_states
self.set_enabled(key, True)
File "/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 113, in set_enabled
self.session.toolbar.set_enabled(enabled, tab, section, display_name)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/manager.py", line 164, in set_enabled
tb.set_enabled(enabled, tab_title, section_title, button_title)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 246, in set_enabled
self.ttb.set_enabled(enabled, tab_title, section_title, button_title)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 496, in set_enabled
raise ValueError(f"Didn't find section '{section_title}' in tab
'{tab_title}'")
ValueError: Didn't find section 'Main' in tab 'ISOLDE'
Populating font family aliases took 519 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
Error processing trigger "new frame":
ValueError: Didn't find section 'Main' in tab 'ISOLDE'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 496, in set_enabled
raise ValueError(f"Didn't find section '{section_title}' in tab
'{tab_title}'")
See log for complete Python traceback.
> cd
> /Users/sconnell/Downloads/GE81112-Oct20201/GE81112/maps/30S-GE81112-PID1604-73/Complex-
> C_MergeAB/Starting_aln_models
Current working directory is:
/Users/sconnell/Downloads/GE81112-Oct20201/GE81112/maps/30S-GE81112-PID1604-73/Complex-
C_MergeAB/Starting_aln_models
> open
> /Users/sconnell/Downloads/GE81112-Oct20201/GE81112/maps/30S-GE81112-PID1604-73/Complex-
> C_MergeAB/Starting_aln_models/Combined_model_001.pdb
Chain information for Combined_model_001.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
v | No description available
> isolde start
> set selectionWidth 4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/cmd/cmd.py", line 29, in isolde_start
get_singleton(session)
File "/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/cmd/cmd.py", line 20, in get_singleton
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=create)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 193, in get_singleton
tinst = tool_class(session, tool_name, **kw)
File "/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/tool.py", line 27, in __init__
isolde = Isolde(session)
File "/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 301, in __init__
session._isolde_tb.isolde_started()
File "/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 136, in isolde_started
self.set_enabled('Start ISOLDE', False)
File "/Users/sconnell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 113, in set_enabled
self.session.toolbar.set_enabled(enabled, tab, section, display_name)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/manager.py", line 164, in set_enabled
tb.set_enabled(enabled, tab_title, section_title, button_title)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 246, in set_enabled
self.ttb.set_enabled(enabled, tab_title, section_title, button_title)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 496, in set_enabled
raise ValueError(f"Didn't find section '{section_title}' in tab
'{tab_title}'")
ValueError: Didn't find section 'Main' in tab 'ISOLDE'
ValueError: Didn't find section 'Main' in tab 'ISOLDE'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 496, in set_enabled
raise ValueError(f"Didn't find section '{section_title}' in tab
'{tab_title}'")
See log for complete Python traceback.
> isolde start
OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac13,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 3,4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
Boot ROM Version: 429.0.0.0.0
SMC Version (system): 2.11f16
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1922)
Kernel Version: Darwin 19.6.0
Time since boot: 24 days 14:56
Graphics/Displays:
NVIDIA GeForce GTX 675MX:
Chipset Model: NVIDIA GeForce GTX 675MX
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 1 GB
Vendor: NVIDIA (0x10de)
Device ID: 0x11a2
Revision ID: 0x00a2
ROM Revision: 3707
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
iMac:
Display Type: LCD
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.18.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.4b1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (3)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Toolbar buttons not created when ISOLDE installed |
comment:3 by , 3 years ago
The ISOLDE bundle's initialize() method creates a little object responsible for managing the states of its toolbar buttons: https://github.com/tristanic/isolde/blob/6155a2aec582cf964119f6d56c99408515cf0fad/isolde/src/__init__.py#L71. That's what's causing the trouble here. For the purposes of this release, I can easily put a try...except around this to pop up a "please restart ChimeraX before using ISOLDE for the first time" message.
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