Opened 13 months ago

Closed 13 months ago

#16066 closed defect (duplicate)

reading AlphaFold JSON as MOLE: KeyError: 'Channels'

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_full_data_0.json"
> "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_full_data_1.json"
> "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_full_data_2.json"
> "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_full_data_3.json"
> "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_full_data_4.json"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mole\\__init__.py", line 27, in open  
return mole.read_mole_json(session, data, file_name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py",
line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
KeyError: 'Channels'  
  
KeyError: 'Channels'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py",
line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
  
See log for complete Python traceback.  
  

> open "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_model_0.cif"
> "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_model_1.cif"
> "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_model_2.cif"
> "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_model_3.cif"
> "C:/Users/2665335/OneDrive - University of Dundee/Desktop/TAU-
> PPP5C/Alphafold/fold_2024_10_03_11_51_model_4.cif"

Chain information for fold_2024_10_03_11_51_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_2024_10_03_11_51_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_2024_10_03_11_51_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_2024_10_03_11_51_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
  
Chain information for fold_2024_10_03_11_51_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
  

> hide #2 models

> show #2 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> hide #3 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> show #3 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> hide #4 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> hide #2 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> hide #3 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> hide #5 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> rainbow #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> color #1 bynucleotide

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
Alignment identifier is 1  
Alignment identifier is 2  

> select #1/A:1-2 #2/A:1-2 #3/A:1-2 #4/A:1-2 #5/A:1-2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
65 atoms, 60 bonds, 10 residues, 5 models selected  

> select #1/A:1-42 #2/A:1-42 #3/A:1-42 #4/A:1-42 #5/A:1-42

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
1620 atoms, 1645 bonds, 210 residues, 5 models selected  
. [ID: 1] region 5 chains [1-42] RMSD: 63.947  
  

> select #1/A:42 #2/A:42 #3/A:42 #4/A:42 #5/A:42

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
45 atoms, 40 bonds, 5 residues, 5 models selected  

> select #1/A:42-200 #2/A:42-200 #3/A:42-200 #4/A:42-200 #5/A:42-200

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
6480 atoms, 6600 bonds, 795 residues, 5 models selected  
. [ID: 1] region 5 chains [42-200] RMSD: 38.640  
  

> select #1/A:1-2 #2/A:1-2 #3/A:1-2 #4/A:1-2 #5/A:1-2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
65 atoms, 60 bonds, 10 residues, 5 models selected  

> select #1/A:1-206 #2/A:1-206 #3/A:1-206 #4/A:1-206 #5/A:1-206

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
8335 atoms, 8490 bonds, 1030 residues, 5 models selected  
. [ID: 1] region 5 chains [1-206] RMSD: 44.997  
  

> select
> #1/A:22-40,44-57,62-75,78-91,96-108,112-125,130-154,161-164,182-184,188-199,206-222,247-257,279-292,307-313,315-322,325-337,363-368,380-386,408-417,438-440,451-453,492-495
> #2/A:22-40,44-57,62-75,78-91,96-108,112-125,130-154,161-164,182-184,188-199,206-222,247-257,279-292,307-313,315-322,325-337,363-368,380-386,408-417,438-440,451-453,492-495
> #3/A:22-40,44-57,62-75,78-91,96-108,112-125,130-154,161-164,182-184,188-199,206-222,247-257,279-292,307-313,315-322,325-337,363-368,380-386,408-417,438-440,451-453,492-495
> #4/A:22-40,44-57,62-75,78-91,96-108,112-125,130-154,161-164,182-184,188-199,206-222,247-257,279-292,307-313,315-322,325-337,363-368,380-386,408-417,438-440,451-453,492-495
> #5/A:22-40,44-57,62-75,78-91,96-108,112-125,130-154,161-164,182-184,188-199,206-222,247-257,279-292,307-313,315-322,325-337,363-368,380-386,408-417,438-440,451-453,492-495

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
9680 atoms, 9770 bonds, 1175 residues, 5 models selected  

> select #1/A:224-230 #2/A:224-230 #3/A:224-230 #4/A:224-230 #5/A:224-230

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
255 atoms, 250 bonds, 35 residues, 5 models selected  

> select #1/A:224-230 #2/A:224-230 #3/A:224-230 #4/A:224-230 #5/A:224-230

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
Error processing trigger "command started":  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\2665335\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.15492.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
255 atoms, 250 bonds, 35 residues, 5 models selected  
. [ID: 1] region 5 chains [224-230] RMSD: 35.932  
  




OpenGL version: 3.3.0 - Build 31.0.101.4887
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 830 13 inch G10 Notebook PC
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 16,794,275,840
MaxProcessMemory: 137,438,953,344
CPU: 12 13th Gen Intel(R) Core(TM) i5-1345U
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 13 months ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → reading AlphaFold JSON as MOLE: KeyError: 'Channels'

comment:2 by Eric Pettersen, 13 months ago

Resolution: → duplicate
Status: assigned → closed
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