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#5747 closed defect (fixed)

ISOLDE vs. 1.4

Reported by:	tclevela@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Infrastructure	Version:
Keywords:		Cc:	Tristan Croll, pett
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18363
ChimeraX Version: 1.4.dev202112080557 (2021-12-08 05:57:49 UTC)
Description
I freshly installed the daily build of ChimeraX and did a fresh install of ISOLDE. These errors get thrown immediately upon trying to launch ISOLDE.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.4.dev202112080557 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_Clipper-0.17.0-cp39-cp39-win_amd64.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: C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\1.4\site-packages  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\1.4\site-packages  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\Python39\Include\ChimeraX-Clipper  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\Include\ChimeraX-
Clipper  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\Python39\Scripts  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\Scripts  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\Thomas\AppData\Local\UCSF\ChimeraX  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python  
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:
C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\Python39\Include\UNKNOWN  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\Include\UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.  
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.4.dev202112080557\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
d:\users\thomas\downloads\chimerax_clipper-0.17.0-cp39-cp39-win_amd64.whl  
Requirement already satisfied: ChimeraX-Core~=1.3rc202112010000 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Clipper==0.17.0) (1.4.dev202112080557)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=4.2 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Clipper==0.17.0) (4.2)  
Requirement already satisfied: ChimeraX-Atomic~=1.31 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Clipper==0.17.0) (1.31.5)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Clipper==0.17.0) (1.0)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (2.6.5)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.1)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (2.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.1)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (2.0.2)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (2.4)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.0)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.0.2)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.5)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.8)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.2.2)  
Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
Clipper==0.17.0) (1.0.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.15.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.0)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
Clipper==0.17.0) (2.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
Clipper==0.17.0) (1.6.1)  
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
Clipper==0.17.0) (1.1)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (2.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (2.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-Clipper==0.17.0) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (2.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
Clipper==0.17.0) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-Clipper==0.17.0) (1.0)  
Installing collected packages: ChimeraX-Clipper  
Successfully installed ChimeraX-Clipper-0.17.0  
\---  

Successfully installed ChimeraX-Clipper-0.17.0  
Installed ChimeraX-Clipper (0.17.0)  
Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-win_amd64.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: C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\1.4\site-packages  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\1.4\site-packages  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\Python39\Include\ChimeraX-ISOLDE  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\Include\ChimeraX-
ISOLDE  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\Python39\Scripts  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\Scripts  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: C:\Users\Thomas\AppData\Local\UCSF\ChimeraX  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python  
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:
C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\Python39\Include\UNKNOWN  
sysconfig: C:\Users\Thomas\AppData\Roaming\Python\Python39\Include\UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.  
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.4.dev202112080557\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
d:\users\thomas\downloads\chimerax_isolde-1.3-cp39-cp39-win_amd64.whl  
Requirement already satisfied: ChimeraX-AtomicLibrary~=4.2 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.3) (4.2)  
Requirement already satisfied: ChimeraX-Clipper~=0.17.0 in
c:\users\thomas\appdata\local\ucsf\chimerax\1.4\site-packages (from ChimeraX-
ISOLDE==1.3) (0.17.0)  
Requirement already satisfied: ChimeraX-Core~=1.3rc202112010000 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.3) (1.4.dev202112080557)  
Requirement already satisfied: ChimeraX-Atomic~=1.31 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.3) (1.31.5)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0.2)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.6.5)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.4)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.2.2)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.8)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0.2)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.5)  
Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.15.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax 1.4.dev202112080557\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Installing collected packages: ChimeraX-ISOLDE  
Successfully installed ChimeraX-ISOLDE-1.3  
\---  

Successfully installed ChimeraX-ISOLDE-1.3  
Installed ChimeraX-ISOLDE (1.3)  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 484, in get_module  
m = importlib.import_module(self.package_name)  
File "C:\Program Files\ChimeraX
1.4.dev202112080557\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\pkg_resources\\__init__.py", line 886, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\pkg_resources\\__init__.py", line 777, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.4.dev202112080557
(c:\program files\chimerax 1.4.dev202112080557\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core~=1.3rc202112010000'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 359, in initialize  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in _get_api  
m = self.get_module()  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 486, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Core 1.4.dev202112080557 (c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core~=1.3rc202112010000'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  

ChimeraX-ISOLDE (installed) [version: 1.3] [api package: chimerax.isolde]
[category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive
Molecular Dynamics Flexible Fitting (iMDFF)]] [command: isolde [categories:
General] [synopsis: Command-line control of ISOLDE simulations]] [command:
rama [categories: General] [synopsis: Live Ramachandran validation of models]]
[command: rota [categories: General] [synopsis: Live rotamer validation of
models]] [command: ~rama [categories: General] [synopsis: Turn off live
Ramachandran validation of models]] [command: ~rota [categories: General]
[synopsis: Turn off live rotamer validation of models]]: custom initialization
failed  

> ui tool show ISOLDE

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 484, in get_module  
m = importlib.import_module(self.package_name)  
File "C:\Program Files\ChimeraX
1.4.dev202112080557\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\Thomas\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\pkg_resources\\__init__.py", line 886, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\pkg_resources\\__init__.py", line 777, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.4.dev202112080557
(c:\program files\chimerax 1.4.dev202112080557\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core~=1.3rc202112010000'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 553, in start_tool  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in _get_api  
m = self.get_module()  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 486, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Core 1.4.dev202112080557 (c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core~=1.3rc202112010000'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\ui\gui.py", line 1672, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2875, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-Core
1.4.dev202112080557 (c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core~=1.3rc202112010000'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-Core
1.4.dev202112080557 (c:\program files\chimerax
1.4.dev202112080557\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core~=1.3rc202112010000'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  
File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To be filled by O.E.M.
Model: To be filled by O.E.M.
OS: Microsoft Windows 10 Pro (Build 18363)
Memory: 34,262,503,424
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD FX(tm)-8350 Eight-Core Processor           
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31.5
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202112080557
    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: 1.0
    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: 1.1
    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: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    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: 1.8
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.15.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (5)

comment:1 by pett, 4 years ago

Cc:	Tristan Croll pett added
Component:	Unassigned → Infrastructure
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE vs. 1.4

comment:2 by pett, 4 years ago

Hi Thomas,

ISOLDE works with the 1.3 release, not the daily build (which is pre-1.4). Unfortunately the 1.3 release is not available on our website. We hope to have that rectified later today.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Greg Couch, 4 years ago

1.3 is available on the website. Reloading the download page should fix it.

in reply to: 4 ; follow-up: 4 comment:4 by tclevela@…, 4 years ago

Hi Eric,

Thanks for the very quick response...I tried to find the 1.3 release at the
time but couldn't, and thought maybe I was just missing it. I see that it's
already up on the website now, and look forward to trying it.

Best,
Tom


Thomas Cleveland
National Institute of Standards and Technology
Biomolecular Measurement Division

On Thu, Dec 9, 2021 at 12:39 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:5 by Greg Couch, 4 years ago

Resolution:	→ fixed
Status:	assigned → closed

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