Opened 4 months ago

Closed 4 months ago

#18124 closed defect (duplicate)

No known data format 'MTZ'

Reported by: sweetb95@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.8.dev202404020138 (2024-04-02 01:38:30 UTC)
Description
I am unable to save or open files, I get an error saying 'Session' object has no attribute 'open_command'

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-OpenCommand' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\manager.py", line 112, in add_provider  
data_format = self.session.data_formats[format_name]  
~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\data_formats\manager.py", line 205, in __getitem__  
raise KeyError("No known data format '%s'" % key)  
KeyError: "No known data format 'mtz'"  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 387, in init_manager  
return api._api_caller.init_manager(api, session, self, name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1298, in init_manager  
return cls._get_func(api, "init_manager")(session, bi, name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\\__init__.py", line 135, in init_manager  
session.open_command = manager.OpenManager(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\manager.py", line 64, in __init__  
super().__init__(name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 992, in __init__  
ts._init_single_manager(self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 871, in
_init_single_manager  
mgr.add_provider(pbi, pvdr, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\manager.py", line 114, in add_provider  
raise ValueError("Database-fetch provider '%s' in bundle %s specified"  
ValueError: Database-fetch provider 'redo' in bundle Map specified unknown
data format 'mtz'  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8.dev202404020138 (2024-04-02)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "G:\\.shortcut-targets-by-id\1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD\Kohout
> Lab\Brandi\alpha
> fold\TPTE2gammaHsVSP1_bc7a6_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> format pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 388, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open C:\Users\brand\Downloads\AF-Q6XPS3-F1-model_v4.pdb format pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 388, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show AlphaFold

> alphafold predict
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
[Repeated 1 time(s)]Alphafold prediction send sequence to Google Colab
returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  

> alphafold search
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  

> open "G:\\.shortcut-targets-by-id\1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD\Kohout
> Lab\Brandi\alpha
> fold\TPTE2gammaHsVSP1_bc7a6_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> format pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 388, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open "G:\\.shortcut-targets-by-id\1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD\Kohout
> Lab\Brandi\alpha
> fold\TPTE2gammaHsVSP1_bc7a6_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> format pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 388, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open "G:\\.shortcut-targets-by-id\1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD\Kohout
> Lab\Brandi\alpha
> fold\TPTE2gammaHsVSP1_bc7a6_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> format pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 388, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> alphafold predict
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK
> directory G:/.shortcut-targets-by-
> id/1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD/Kohout Lab/Brandi/alpha
> fold/TPTE2gammaHsVSP1_bc7a6_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb
> templates true

Expected a keyword  

> alphafold predict
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK
> directory G:/.shortcut-targets-by-
> id/1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD/Kohout Lab/Brandi/alpha
> fold/TPTE2gammaHsVSP1_bc7a6_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb
> minimize true

Expected a keyword  

No sequence chosen for AlphaFold predict  

> alphafold predict
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK
> directory G:/.shortcut-targets-by-
> id/1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD/Kohout Lab/Brandi/alpha
> fold/TPTE2gammaHsVSP1_bc7a6_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb
> minimize true

Expected a keyword  

> alphafold predict
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK
> directory G:/.shortcut-targets-by-
> id/1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD/Kohout Lab/Brandi/alpha
> fold/TPTE2gammaHsVSP1_bc7a6_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb
> minimize true

Expected a keyword  

> ui tool show AlphaFold

> alphafold predict
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK

Running AlphaFold prediction  
[Repeated 1 time(s)]Alphafold prediction send sequence to Google Colab
returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  

> alphafold predict
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK

Running AlphaFold prediction  
[Repeated 1 time(s)]Alphafold prediction send sequence to Google Colab
returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  

> alphafold predict
> MNESPQTNEFKGTTEEAPAKESPHTSEFKGAALVSPISKSMLERLSKFEVEDAENVASYDSKIKKIVHSIVSSFAFGIFGVFLVLLDVTLLLADLIFTDSKLYIPLEYRSISLAIGLFFLMDVLLRVFVEGRQQYFSDLFNILDTAIIVIPLLVDVIYIFFDIKLLRNIPRWTHLVRLLRLIILIRIFHLLHQKRQLEKLMRRLVSENKRRYTRDGFDLDLTYVTERIIAMSFPSSGRQSFYRNPIEEVVRFLDKKHRNHYRVYNLCSERAYDPKHFHNRVSRIMIDDHNVPTLHEMVVFTKEVNEWMAQDLENIVAIHCKGGKGRTGTMVCALLIASEIFLTAEESLYYFGERRTNKTHSNKFQGVETPSQNRYVGYFAQVKHLYNWNLPPRRILFIKRFIIYSIRGDVCDLKVQVVMEKKVVFSSTSLGNCSILHDIETDKILINVYDGPPLYDDVKVQFFSSNLPKYYDNCPFFFWFNTSFIQNNRLCLPRNELDNPHKQKAWKIYPPEFAVEILFGEK

Running AlphaFold prediction  
[Repeated 1 time(s)]Alphafold prediction send sequence to Google Colab
returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  
Running AlphaFold prediction  
Alphafold prediction send sequence to Google Colab returned: None  
Running AlphaFold prediction  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 28, in _file_open  
show_open_file_dialog(session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 299, in show_open_file_dialog  
file_filters, openable_formats, no_filter = make_qt_name_filters(session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 277, in make_qt_name_filters  
openable_formats = [fmt for fmt in session.open_command.open_data_formats if
fmt.suffixes]  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 277, in make_qt_name_filters  
openable_formats = [fmt for fmt in session.open_command.open_data_formats if
fmt.suffixes]  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 28, in _file_open  
show_open_file_dialog(session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 299, in show_open_file_dialog  
file_filters, openable_formats, no_filter = make_qt_name_filters(session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 277, in make_qt_name_filters  
openable_formats = [fmt for fmt in session.open_command.open_data_formats if
fmt.suffixes]  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 277, in make_qt_name_filters  
openable_formats = [fmt for fmt in session.open_command.open_data_formats if
fmt.suffixes]  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 268, in <lambda>  
lambda *args, ses=session: show_open_file_dialog(ses), tool_tip="Open input
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 299, in show_open_file_dialog  
file_filters, openable_formats, no_filter = make_qt_name_filters(session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 277, in make_qt_name_filters  
openable_formats = [fmt for fmt in session.open_command.open_data_formats if
fmt.suffixes]  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 277, in make_qt_name_filters  
openable_formats = [fmt for fmt in session.open_command.open_data_formats if
fmt.suffixes]  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
AlphaFold prediction finished  
Results in C:\Users\brand/Downloads/ChimeraX/AlphaFold/prediction_1  

> open C:\Users\brand/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 268, in <lambda>  
lambda *args, ses=session: show_open_file_dialog(ses), tool_tip="Open input
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 299, in show_open_file_dialog  
file_filters, openable_formats, no_filter = make_qt_name_filters(session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 277, in make_qt_name_filters  
openable_formats = [fmt for fmt in session.open_command.open_data_formats if
fmt.suffixes]  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 277, in make_qt_name_filters  
openable_formats = [fmt for fmt in session.open_command.open_data_formats if
fmt.suffixes]  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open "G:/.shortcut-targets-by-id/1fVamgI_QfWYzNrgDc5LXDGQULUArsCCD/Kohout
> Lab/Brandi/ChimeraX/ChimeraX edited files/G214C VSD dimerization.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 662, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 2027, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 79, in cmd_open  
mgr = session.open_command  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 34, in display  
self._customize_dialog(session, dialog)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 95, in _customize_dialog  
self._format_selected(session, dialog)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 104, in _format_selected  
self._current_option = save_mgr.save_args_widget(fmt) or
self._no_options_label  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\manager.py", line 113, in save_args_widget  
return bi.run_provider(self.session, provider_info.format_name,
self).save_args_widget(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 31, in run_provider  
if mgr == session.open_command:  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 31, in run_provider  
if mgr == session.open_command:  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 34, in display  
self._customize_dialog(session, dialog)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 95, in _customize_dialog  
self._format_selected(session, dialog)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 104, in _format_selected  
self._current_option = save_mgr.save_args_widget(fmt) or
self._no_options_label  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\manager.py", line 113, in save_args_widget  
return bi.run_provider(self.session, provider_info.format_name,
self).save_args_widget(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 31, in run_provider  
if mgr == session.open_command:  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 31, in run_provider  
if mgr == session.open_command:  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 34, in display  
self._customize_dialog(session, dialog)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 95, in _customize_dialog  
self._format_selected(session, dialog)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 104, in _format_selected  
self._current_option = save_mgr.save_args_widget(fmt) or
self._no_options_label  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\manager.py", line 113, in save_args_widget  
return bi.run_provider(self.session, provider_info.format_name,
self).save_args_widget(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 31, in run_provider  
if mgr == session.open_command:  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Session' object has no attribute 'open_command'  
  
AttributeError: 'Session' object has no attribute 'open_command'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 31, in run_provider  
if mgr == session.open_command:  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.5972
OpenGL renderer: Intel(R) Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: HP
Model: HP Envy x360 2-in-1 Laptop 16-ac0xxx
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,587,612,160
MaxProcessMemory: 137,438,953,344
CPU: 14 Intel(R) Core(TM) Ultra 7 155U
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.6.0
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56.1
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    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: 2.12.1
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    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: 1.8.dev202404020138
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    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-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    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-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.37.1
    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-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.3.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    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: 0.6.1
    tables: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 4 months ago

Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → No known data format 'MTZ'

comment:2 by pett, 4 months ago

Resolution: → duplicate
Status: accepted → closed

Hi Brandi,

Thanks for reporting this problem. It has been fixed in more recent versions of ChimeraX, so if you get the current production release then it won't happen to you anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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