ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.4-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb format pdb

1pso_Pepsin-1-1.pdb title:  
The crystal structure of human pepsin and its complex with pepstatin [more
info...]  
  
Chain information for 1pso_Pepsin-1-1.pdb #1  
---  
Chain | Description | UniProt  
E | pepsin 3A | PEPA_HUMAN 1-326  
I | pepstatin |   
  
Non-standard residues in 1pso_Pepsin-1-1.pdb #1  
---  
IVA — isovaleric acid  
STA — statine  
  

> hide atoms

[Repeated 1 time(s)]

> fetch

Unknown command: fetch  

> File

Unknown command: File  

> Fetch

Unknown command: Fetch  

> hide target m

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> ui tool show "Selection Inspector"

Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  

> open /Users/yusrajuwale/Downloads/mellittin_2mlt-1-1.pdb format pdb

mellittin_2mlt-1-1.pdb title:  
Melittin [more info...]  
  
Chain information for mellittin_2mlt-1-1.pdb #2  
---  
Chain | Description | UniProt  
A B | melittin | MEL_APIME 1-26  
  
Non-standard residues in mellittin_2mlt-1-1.pdb #2  
---  
NH2 — amino group  
SO4 — sulfate ion  
  

> select #2/B:1-27

201 atoms, 203 bonds, 27 residues, 1 model selected  

> select #2/A:1-27

201 atoms, 203 bonds, 27 residues, 1 model selected  

> open /Users/yusrajuwale/Downloads/mellittin_2mlt-1-1.pdb format pdb

mellittin_2mlt-1-1.pdb title:  
Melittin [more info...]  
  
Chain information for mellittin_2mlt-1-1.pdb #3  
---  
Chain | Description | UniProt  
A B | melittin | MEL_APIME 1-26  
  
Non-standard residues in mellittin_2mlt-1-1.pdb #3  
---  
NH2 — amino group  
SO4 — sulfate ion  
  

> open P01501 fromDatabase uniprot associate #3/A,B

Summary of feedback from opening P01501 fetched from uniprot  
---  
notes | Fetching compressed P01501 UniProt info from https://www.uniprot.org/uniprot/P01501.xml  
Alignment identifier is P01501  
Associated mellittin_2mlt-1-1.pdb chain A to P01501 with 0 mismatches  
Associated mellittin_2mlt-1-1.pdb chain B to P01501 with 0 mismatches  
  
Opened UniProt P01501  

> select #3/A-B:2-11,13-18,21-25

322 atoms, 318 bonds, 42 residues, 1 model selected  

> select ~sel & ##selected

113 atoms, 96 bonds, 37 residues, 1 model selected  

> hide #3 models

> sequence chain #3/A,B

Alignment identifier is 1  

> select down

113 atoms, 96 bonds, 37 residues, 1 model selected  

> color #2 bynucleotide

> select #3/A-B:2-11,13-18,21-25

322 atoms, 318 bonds, 42 residues, 1 model selected  

> select clear

[Repeated 2 time(s)]

> show #2 target m

> sequence chain #1/E

Alignment identifier is 1/E  

> sequence chain #1/I

Alignment identifier is 1/I  

> sequence chain #2/A,B#3/A,B

Alignment identifier is 2  

> sequence chain #1/E

Alignment identifier is 1/E  

> sequence chain #1/I

Alignment identifier is 1/I  

> sequence chain #2/A,B#3/A,B

Alignment identifier is 1  

> select
> #1/E:2-5,7-9,13-20,25-32,39-41,70-74,79-87,89-91,94-96,99-106,119-122,150-154,164-167,180-183,191-194,196-199,202-205,210-214,221-223,258-262,265-269,275-278,281-284,286-288,299-301,309-314,319-324

996 atoms, 996 bonds, 127 residues, 1 model selected  

> select #1/I:1

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

> select #1/I:1-6

48 atoms, 47 bonds, 6 residues, 1 model selected  

> select #1/I:6

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/I:6

12 atoms, 11 bonds, 1 residue, 1 model selected  

> hide #2 models

> show #3 models

> sequence chain #1/I

Alignment identifier is 1/I  

> hide #3 models

> select add #1

2720 atoms, 2546 bonds, 566 residues, 1 model selected  

> show #2 models

> select add #2

3155 atoms, 2960 bonds, 645 residues, 2 models selected  

> select subtract #1

435 atoms, 414 bonds, 79 residues, 1 model selected  

> sequence chain #2/A,B

Alignment identifier is 1  

> select #2/A-B:3

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select #2/A-B:3-9

96 atoms, 94 bonds, 14 residues, 1 model selected  

> select add #2

435 atoms, 414 bonds, 79 residues, 1 model selected  

> sequence chain #2/A,B

Alignment identifier is 1  

> select subtract #2

Nothing selected  

> hide #2 models

> show #3 models

> hide #3 models

> open /Users/yusrajuwale/Downloads/mellittin_2mlt-1-1.pdb

mellittin_2mlt-1-1.pdb title:  
Melittin [more info...]  
  
Chain information for mellittin_2mlt-1-1.pdb #4  
---  
Chain | Description | UniProt  
A B | melittin | MEL_APIME 1-26  
  
Non-standard residues in mellittin_2mlt-1-1.pdb #4  
---  
NH2 — amino group  
SO4 — sulfate ion  
  

> open /Users/yusrajuwale/Downloads/mellittin_2mlt-1-1.pdb

mellittin_2mlt-1-1.pdb title:  
Melittin [more info...]  
  
Chain information for mellittin_2mlt-1-1.pdb #5  
---  
Chain | Description | UniProt  
A B | melittin | MEL_APIME 1-26  
  
Non-standard residues in mellittin_2mlt-1-1.pdb #5  
---  
NH2 — amino group  
SO4 — sulfate ion  
  

> style #4-5 stick

Changed 870 atom styles  

> hide #5 models

> hide #4 models

Desktop color scheme is dark  

> ui tool show "Selection Inspector"

> open /Users/yusrajuwale/Downloads format dicom

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/__init__.py", line 36, in run_provider  
actions.run_provider(session, name)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/actions.py", line 29, in run_provider  
open_dicom(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/actions.py", line 37, in open_dicom  
show_open_folder_dialog(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 370, in
show_open_folder_dialog  
_folder_dlg.display(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 118, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_opener.py", line 7, in open  
dcm = DICOM.from_paths(session, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 43, in from_paths  
return cls(path, session=session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 38, in __init__  
self.find_dicom_files(self.paths)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 90, in find_dicom_files  
dfiles.extend(self._find_dicom_files_in_directory_recursively(path))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 141, in
_find_dicom_files_in_directory_recursively  
for d in dirs:  
^^^^  
UnboundLocalError: cannot access local variable 'dirs' where it is not
associated with a value  
  
UnboundLocalError: cannot access local variable 'dirs' where it is not
associated with a value  
  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 141, in
_find_dicom_files_in_directory_recursively  
for d in dirs:  
^^^^  
  
See log for complete Python traceback.  
  

> open /Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb format pdb

Cannot open '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb': [Errno 1]
Operation not permitted: '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb'  

> open /Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb format pdb

Cannot open '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb': [Errno 1]
Operation not permitted: '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb'  

> open /Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb format pdb

Cannot open '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb': [Errno 1]
Operation not permitted: '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb'  

> open /Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb format pdb

Cannot open '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb': [Errno 1]
Operation not permitted: '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb'  

> open /Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb format pdb

Cannot open '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb': [Errno 1]
Operation not permitted: '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb'  

> open /Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb format pdb

Cannot open '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb': [Errno 1]
Operation not permitted: '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb'  

> open /Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb format pdb

Cannot open '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb': [Errno 1]
Operation not permitted: '/Users/yusrajuwale/Downloads/1pso_Pepsin-1-1.pdb'  

> open /Users/yusrajuwale/Downloads format dicom

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/__init__.py", line 36, in run_provider  
actions.run_provider(session, name)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/actions.py", line 29, in run_provider  
open_dicom(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/actions.py", line 37, in open_dicom  
show_open_folder_dialog(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 370, in
show_open_folder_dialog  
_folder_dlg.display(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 118, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_opener.py", line 7, in open  
dcm = DICOM.from_paths(session, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 43, in from_paths  
return cls(path, session=session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 38, in __init__  
self.find_dicom_files(self.paths)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 90, in find_dicom_files  
dfiles.extend(self._find_dicom_files_in_directory_recursively(path))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 141, in
_find_dicom_files_in_directory_recursively  
for d in dirs:  
^^^^  
UnboundLocalError: cannot access local variable 'dirs' where it is not
associated with a value  
  
UnboundLocalError: cannot access local variable 'dirs' where it is not
associated with a value  
  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 141, in
_find_dicom_files_in_directory_recursively  
for d in dirs:  
^^^^  
  
See log for complete Python traceback.  
  

> volume projectionMode 3d

No volumes specified  

> open /Users/yusrajuwale/Downloads/mellittin_2mlt-1-1.pdb format pdb

Cannot open '/Users/yusrajuwale/Downloads/mellittin_2mlt-1-1.pdb': [Errno 1]
Operation not permitted: '/Users/yusrajuwale/Downloads/mellittin_2mlt-1-1.pdb'  

> show #1 models

> hide #1 models

> show #2 models

> open /Users/yusrajuwale/Downloads format dicom

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/__init__.py", line 36, in run_provider  
actions.run_provider(session, name)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/actions.py", line 29, in run_provider  
open_dicom(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/medical_toolbar/actions.py", line 37, in open_dicom  
show_open_folder_dialog(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 370, in
show_open_folder_dialog  
_folder_dlg.display(session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 118, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom_opener.py", line 7, in open  
dcm = DICOM.from_paths(session, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 43, in from_paths  
return cls(path, session=session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 38, in __init__  
self.find_dicom_files(self.paths)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 90, in find_dicom_files  
dfiles.extend(self._find_dicom_files_in_directory_recursively(path))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 141, in
_find_dicom_files_in_directory_recursively  
for d in dirs:  
^^^^  
UnboundLocalError: cannot access local variable 'dirs' where it is not
associated with a value  
  
UnboundLocalError: cannot access local variable 'dirs' where it is not
associated with a value  
  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom.py", line 141, in
_find_dicom_files_in_directory_recursively  
for d in dirs:  
^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: MLXY3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4 (22F66)
      Kernel Version: Darwin 22.5.0
      Time since boot: 5 days, 5 hours, 12 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0