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#15264 assigned defect

Problem installing/running XMAS

Reported by:	saar@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Tool Shed	Version:
Keywords:		Cc:	Zach Pearson, Richard Scheltema
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
i cannot run XMAS 

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> devel install C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-
> main\ChimeraX_XMAS_bundle-main

running build  
running build_py  
running bdist_wheel  
installing to build\bdist.win-amd64\wheel  
running install  
running install_lib  
warning: install_lib: 'build\lib' does not exist -- no Python modules to
install  
  
running install_egg_info  
running egg_info  
writing ChimeraX_XMAS.egg-info\PKG-INFO  
writing dependency_links to ChimeraX_XMAS.egg-info\dependency_links.txt  
writing top-level names to ChimeraX_XMAS.egg-info\top_level.txt  
reading manifest file 'ChimeraX_XMAS.egg-info\SOURCES.txt'  
writing manifest file 'ChimeraX_XMAS.egg-info\SOURCES.txt'  
Copying ChimeraX_XMAS.egg-info to build\bdist.win-
amd64\wheel\\.\ChimeraX_XMAS-1.1.3-py3.11.egg-info  
running install_scripts  
creating build\bdist.win-amd64\wheel\ChimeraX_XMAS-1.1.3.dist-info\WHEEL  
creating 'dist\ChimeraX_XMAS-1.1.3-py3-none-any.whl' and adding
'build\bdist.win-amd64\wheel' to it  
adding 'ChimeraX_XMAS-1.1.3.dist-info/METADATA'  
adding 'ChimeraX_XMAS-1.1.3.dist-info/WHEEL'  
adding 'ChimeraX_XMAS-1.1.3.dist-info/top_level.txt'  
adding 'ChimeraX_XMAS-1.1.3.dist-info/RECORD'  
removing build\bdist.win-amd64\wheel  
Distribution is in C:\Users\saar\Desktop\dist\ChimeraX_XMAS-1.1.3-py3-none-
any.whl  
[toolshed install](help:user/commands/toolshed.html#install)  
C:\Users\saar\Desktop\dist\ChimeraX_XMAS-1.1.3-py3-none-any.whl reinstall true  
  
[toolshed install C:\Users\saar\Desktop\dist\ChimeraX_XMAS-1.1.3-py3-none-  
any.whl reinstall true](cxcmd:toolshed install  
C:\\\Users\\\saar\\\Desktop\\\dist\\\ChimeraX_XMAS-1.1.3-py3-none-any.whl
reinstall  
true)  
  
tried to get metadata for package installed in editable mode ('ChimeraX-XMAS')
but could not find the package's finder.py or path file  
Installed ChimeraX-XMAS (1.1.3)  
  

> installC:\Users\saar\Downloads\ChimeraX_TestManager-
> master.zip\ChimeraX_TestManager-master

Unknown command: devel installC:\Users\saar\Downloads\ChimeraX_TestManager-
master.zip\ChimeraX_TestManager-master  

> C:\Users\saar\Downloads\ChimeraX_TestManager-
> master.zip\ChimeraX_TestManager-master

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_TestManager-master.zip\ChimeraX_TestManager-
master' does not exist  

> C:\Users\saar\Downloads\ChimeraX_TestManager-
> master.zip\ChimeraX_TestManager-master

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_TestManager-master.zip\ChimeraX_TestManager-
master' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> installC:\Users\saar\Downloads\ChimeraX_XMAS_bundle-
> main.zip\ChimeraX_XMAS_bundle-main

Unknown command: devel installC:\Users\saar\Downloads\ChimeraX_XMAS_bundle-
main.zip\ChimeraX_XMAS_bundle-main  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> open C:/Users/saar/Downloads/6e7k.pdb

6e7k.pdb title:  
Structure of the lipoprotein lipase GPIHBP1 complex that mediates plasma
triglyceride hydrolysis [more info...]  
  
Chain information for 6e7k.pdb #1  
---  
Chain | Description | UniProt  
A B | LPL | LIPL_HUMAN 28-475  
C D | glycosylphosphatidylinositol-anchored high density lipoprotein-binding
protein 1 | HDBP1_HUMAN 21-151  
  
Non-standard residues in 6e7k.pdb #1  
---  
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)  
CA — calcium ion  
FUC — α-L-fucopyranose (α-L-fucose; 6-deoxy-α-L-galactopyranose; L-fucose;
fucose)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> ui tool show XMAS

Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1142, in _find_and_load_unlocked  
ModuleNotFoundError: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
570, in start_tool  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-XMAS's
module: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 1723, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\run.py", line
49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\cli.py", line
2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\cmd.py", line 219, in
ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> ui tool show XMAS

Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1142, in _find_and_load_unlocked  
ModuleNotFoundError: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
570, in start_tool  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-XMAS's
module: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 1723, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\run.py", line
49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\cli.py", line
2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\cmd.py", line 219, in
ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> ui tool show XMAS

Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1142, in _find_and_load_unlocked  
ModuleNotFoundError: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
570, in start_tool  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-XMAS's
module: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 1723, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\run.py", line
49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\cli.py", line
2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\cmd.py", line 219, in
ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> open C:/Users/saar/Downloads/SRCH=27108--groups--
> MAN.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.PEPLEN=1.PASS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=50.9-79.GROUPS=NA.PRIMARYSCORE=objectObject.csv

Unrecognized file suffix '.csv'  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
> main

Missing or invalid "path" argument: File
'C:\Users\saar\Downloads\ChimeraX_XMAS_bundle-main.zip\ChimeraX_XMAS_bundle-
main' does not exist  

> ui tool show XMAS

Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1142, in _find_and_load_unlocked  
ModuleNotFoundError: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
570, in start_tool  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-XMAS's
module: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 1723, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\run.py", line
49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\cli.py", line
2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\cmd.py", line 219, in
ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show XMAS

Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1142, in _find_and_load_unlocked  
ModuleNotFoundError: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
570, in start_tool  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-XMAS's
module: No module named 'chimerax.XMAS'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 1723, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\run.py", line
49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\cli.py", line
2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\ui\cmd.py", line 219, in
ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
Error importing bundle ChimeraX-XMAS's module: No module named 'chimerax.XMAS'  
  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 546.59
OpenGL renderer: Quadro P400/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: da_DK.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP Z2 Tower G4 Workstation
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 17,018,552,320
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 18 months ago

Cc:	Zach Pearson Richard Scheltema added
Component:	Unassigned → Tool Shed
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Problem installing/running XMAS

Reported by Samina

comment:2 by Greg Couch, 18 months ago

Just wondering what led to to "devel install" instead of "toolshed install"? "devel install" is for developers installing a local build. You should be using "toolshed install" to install a downloaded bundle. Or you could click on "More Tools..." in the Tools menu, search for the XMAS bundle, and then click on the Install button.

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