Opened 19 months ago

Closed 19 months ago

#14890 closed defect (duplicate)

KeyError: "No known data format 'mtz'"

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tom Goddard
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: 1.8.dev202404020138 (2024-04-02 01:38:30 UTC)
Description
(Describe the actions that caused this problem to occur here)

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  
  
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  

> ui tool show AlphaFold

> alphafold predict
> QLNLKVEFYNSQPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSQGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSQYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWGKEPGGSVVPSTQPVTTPPATTKPPATTIPPSGAGGGSGGGSGGGSAGGGENLYFQGMAAGSITTLPSLPEDGGSGAFPPGHFKDPKRLYCKNGGFFLRIHPDGRVDGVREKSDPHIKLQLQAEERGVVSIKGVCANRYLAMKEDGRLLASKCVTDECFFFERLESNNYNTYRSRKYSSWYVALKRTGQYKLGPKTGPGQKAILFLPMSAKSKDEL

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\Boris-BB/Downloads/ChimeraX/AlphaFold/prediction_1  

> open C:\Users\Boris-
> BB/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> color #1 #55aa00ff

> color #1 #00557fff

> color #1 #00aaffff

> color #1 #ffaa00ff

> color #1 #55ff7fff

QPixmap::scaled: Pixmap is a null pixmap  

Alignment identifier is 1/A  

> select /A:186

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:186-203

80 atoms, 79 bonds, 18 residues, 1 model selected  

> color sel bychain

[Repeated 1 time(s)]

> color sel byhetero

[Repeated 1 time(s)]

> color sel bychain

> color #1 #aaaa00ff

> log metadata #1

The model has no metadata

> log chains #1

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> view clip false

[Repeated 1 time(s)]

> show target m

> select /A:180

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:180

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:186

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:186-203

80 atoms, 79 bonds, 18 residues, 1 model selected  

> color bfactor sel

80 atoms, 18 residues, atom bfactor range 30.3 to 44.2  

> color bfactor sel

80 atoms, 18 residues, atom bfactor range 30.3 to 44.2  

> color sel bynucleotide

> hide sel cartoons

> show sel cartoons

> hide sel surfaces

> show sel cartoons

> hide sel atoms

> hide sel cartoons

[Repeated 1 time(s)]

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

[Repeated 1 time(s)]

> show sel surfaces

> select /A:204

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select
> /A:4-10,22-28,39-45,53-63,69-71,76-82,92-98,108-117,143-147,150-153,240-244,250-253,259-262,272-278,281-286,292-295,301-304,313-317,323-327,358-362

982 atoms, 990 bonds, 117 residues, 1 model selected  

> select
> /A:4-10,22-28,39-45,53-63,69-71,76-82,92-98,108-117,143-147,150-153,240-244,250-253,259-262,272-278,281-286,292-295,301-304,313-317,323-327,358-362

982 atoms, 990 bonds, 117 residues, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select
> /A:4-10,22-28,39-45,53-63,69-71,76-82,92-98,108-117,143-147,150-153,240-244,250-253,259-262,272-278,281-286,292-295,301-304,313-317,323-327,358-362

982 atoms, 990 bonds, 117 residues, 1 model selected  

> select
> /A:4-10,22-28,39-45,53-63,69-71,76-82,92-98,108-117,143-147,150-153,240-244,250-253,259-262,272-278,281-286,292-295,301-304,313-317,323-327,358-362

982 atoms, 990 bonds, 117 residues, 1 model selected  

> select /A:36-38,73-75,125-127,268-270,309-311,346-348,354-356,366-368

183 atoms, 178 bonds, 24 residues, 1 model selected  

> select /A:36-38,73-75,125-127,268-270,309-311,346-348,354-356,366-368

183 atoms, 178 bonds, 24 residues, 1 model selected  

> select /A:186

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:186-203

80 atoms, 79 bonds, 18 residues, 1 model selected  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

[Repeated 2 time(s)]

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor gray

> set bgColor #80808000

> set bgColor white

> set bgColor #ffffff00

> set bgColor gray

> set bgColor #80808000

> select /A:204

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  
Position Coverage for "structure strands"  
---  
Alignment | 4-10,22-28,39-45,53-63,69-71,76-82,92-98,108-117,143-147,150-153,240-244,250-253,259-262,272-278,281-286,292-295,301-304,313-317,323-327,358-362  
chain A | 4-10,22-28,39-45,53-63,69-71,76-82,92-98,108-117,143-147,150-153,240-244,250-253,259-262,272-278,281-286,292-295,301-304,313-317,323-327,358-362  
/A | LEU 4-ASN 10,PRO 22-ASN 28,LEU 39-TYR 45,GLN 53-ILE 63,TYR 69-GLY 71,VAL 76-LYS 82,THR 92-PHE 98,HIS 108-LYS 117,VAL 143-LEU 147,VAL 150-TRP 153,LYS 240-CYS 244,PHE 250-ILE 253,VAL 259-VAL 262,LEU 272-GLU 278,VAL 281-GLY 286,TYR 292-MET 295,LEU 301-SER 304,PHE 313-LEU 317,ASN 323-SER 327,PHE 358-SER 362  
  

> select add #1

2814 atoms, 2884 bonds, 369 residues, 2 models selected  

> select subtract #1

1 model selected  

> hide #1.1 models

> show #1.1 models

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> color (#!1 & sel) medium blue

> select /A:185

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:1-185

1425 atoms, 1463 bonds, 185 residues, 1 model selected  

> color (#!1 & sel) hot pink

> select /A:204

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:204-209

57 atoms, 58 bonds, 6 residues, 1 model selected  

> select /A:204-209

57 atoms, 58 bonds, 6 residues, 1 model selected  

> select /A:204

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:204-210

61 atoms, 62 bonds, 7 residues, 1 model selected  

> color (#!1 & sel) light sea green

> color #1.1 #55ff7fff

> color #1.1 #55aa00ff

> select /A:211

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:211-369

1248 atoms, 1277 bonds, 159 residues, 1 model selected  

> color (#!1 & sel) orange

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set bgColor gray

> set bgColor #80808000

> color (#!1 & sel) red

> select /A:211-369

1248 atoms, 1277 bonds, 159 residues, 1 model selected  

> cd C:/Users/Boris-BB/Desktop/ChimeraX

Current working directory is: C:\Users\Boris-BB\Desktop\ChimeraX  
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\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 38, in _file_save  
show_save_file_dialog(session)  
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.  
  

> save C:\Users\Boris-BB/Desktop\image1.png supersample 3

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\shortcuts\\__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1296, in save_image  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run  
run_command(session, command, **kw)  
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\save_command\cmd.py", line 51, in cmd_save  
provider_args = mgr.save_args(data_format)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\manager.py", line 92, in save_args  
return provider_info.bundle_info.run_provider(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\image_formats\\__init__.py", line 33, 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\image_formats\\__init__.py", line 33, 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\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.  
  

> save C:\Users\Boris-BB/Desktop\image1.png supersample 3

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\shortcuts\\__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1296, in save_image  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run  
run_command(session, command, **kw)  
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\save_command\cmd.py", line 51, in cmd_save  
provider_args = mgr.save_args(data_format)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\manager.py", line 92, in save_args  
return provider_info.bundle_info.run_provider(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\image_formats\\__init__.py", line 33, 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\image_formats\\__init__.py", line 33, 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 31.0.101.4953
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

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

Manufacturer: Dell Inc.
Model: Latitude 5420
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,912,879,616
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
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: 1.2.1
    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 Eric Pettersen, 19 months ago

Cc: Tom Goddard added
Component: Unassigned → Tool Shed
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → KeyError: "No known data format 'mtz'"

comment:2 by Eric Pettersen, 19 months ago

Resolution: → duplicate
Status: accepted → closed
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