Open DCM/DICOM: handler is missing required dependencies

[k8702186@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Attempted to open a dcm dicom image

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
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  
Enter a AlphaFold database ID in the entry field  

> open P29474 fromDatabase alphafold format mmcif

Summary of feedback from opening P29474 fetched from alphafold  
---  
notes | Fetching compressed AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold P29474 from
https://alphafold.ebi.ac.uk/files/AF-P29474-F1-model_v6.cif  
  
Chain information for AlphaFold P29474 #1  
---  
Chain | Description | UniProt  
A | Nitric oxide synthase 3 | NOS3_HUMAN 1-1203  
  
Color AlphaFold P29474 by residue attribute pLDDT_score  
Drag select of 26 residues  

> open 2gbp fromDatabase pdb format mmcif

Summary of feedback from opening 2gbp fetched from pdb  
---  
notes | Fetching compressed mmCIF 2gbp from http://files.rcsb.org/download/2gbp.cif  
Fetching CCD BGC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/BGC/BGC.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
  
2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #2  
---  
Chain | Description | UniProt  
A | D-GALACTOSE/D-GLUCOSE BINDING PROTEIN | DGAL_ECOLI 1-309  
  
Non-standard residues in 2gbp #2  
---  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
CA — calcium ion  
  

> show sel target ab

> close session

> open
> "D:/iCloudDrive/AI_JKU_iCloudExchange/JKU_HDS_AI_master/2025_WS_BioSequence
> Analysis VO und UE/Assignment5_Databases/P17276.fasta"

Summary of feedback from opening
D:/iCloudDrive/AI_JKU_iCloudExchange/JKU_HDS_AI_master/2025_WS_BioSequence
Analysis VO und UE/Assignment5_Databases/P17276.fasta  
---  
note | Alignment identifier is P17276.fasta  
  
Opened 1 sequence from P17276.fasta  

> open
> "D:\iCloudDrive\AI_JKU_iCloudExchange\JKU_HDS_AI_master\2025_WS_BioSequence
> Analysis VO und UE\Assignment5_Databases\P17276.fasta" format fasta

Summary of feedback from opening
D:\iCloudDrive\AI_JKU_iCloudExchange\JKU_HDS_AI_master\2025_WS_BioSequence
Analysis VO und UE\Assignment5_Databases\P17276.fasta  
---  
notes | Destroying pre-existing alignment with identifier P17276.fasta  
Alignment identifier is P17276.fasta  
  
Opened 1 sequence from P17276.fasta  

> open caffeine fromDatabase iupac format iupac

Translated IUPAC name to SMILES string via Cambridge web service (IUPAC:
caffeine)  
Translated SMILES to 3D structure via NCI web service (SMILES:
N1(C)C(=O)N(C)C=2N=CN(C)C2C1=O)  

> style sphere

Changed 24 atom styles  

> style ball

Changed 24 atom styles  

> style stick

Changed 24 atom styles  

> style ball

Changed 24 atom styles  

> style sphere

Changed 24 atom styles  

> style stick

Changed 24 atom styles  

> hide cartoons

[Repeated 1 time(s)]

> show cartoons

[Repeated 1 time(s)]

> hide atoms

[Repeated 1 time(s)]

> show atoms

> lighting full

> lighting soft

> lighting simple

> ui mousemode right select

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right "mark maximum"

> ui mousemode right "mark plane"

> ui mousemode right "mark surface"

> ui mousemode right "mark center"

> ui mousemode right "mark point"

[Repeated 1 time(s)]

> ui mousemode right "mark maximum"

> ui mousemode right "link markers"

> ui mousemode right "resize markers"

> ui mousemode right "link markers"

> ui mousemode right "mark maximum"

> cartoon

> cartoon hide

> select backbone

Nothing selected  

> show atoms

> select all

24 atoms, 25 bonds, 1 residue, 1 model selected  

> color bfactor sel

24 atoms, 1 residues, atom bfactor range 0 to 0  

> color bfactor sel

24 atoms, 1 residues, atom bfactor range 0 to 0  

> color bfactor sel

24 atoms, 1 residues, atom bfactor range 0 to 0  

> undo

[Repeated 1 time(s)]

> color bfactor sel

24 atoms, 1 residues, atom bfactor range 0 to 0  

> style sel stick

Changed 24 atom styles  

> undo

[Repeated 2 time(s)]

> ~hbonds

[Repeated 1 time(s)]

> show sel surfaces

[Repeated 1 time(s)]

> hide sel surfaces

> show sel atoms

> hide sel atoms

> show sel atoms

> ui tool show "Side View"

[Repeated 1 time(s)]

> help help:user

> select aromatic-ring

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

> select clear

> select backbone

Nothing selected  

> toolshed show

> open
> D:/iCloudDrive/HDS_Private_Xchange/Personal_Docs/2025-02_Ges_Sonografie_thromb
> format dicom

Summary of feedback from opening
D:/iCloudDrive/HDS_Private_Xchange/Personal_Docs/2025-02_Ges_Sonografie_thromb  
---  
note | Pydicom could not read invalid or non-DICOM file AUT573373.202502030881.zip; skipping.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 270, in <lambda>  
lambda *args, ses=session: show_open_folder_dialog(ses), tool_tip="Open folder
data",  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 370, in
show_open_folder_dialog  
_folder_dlg.display(session)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 118, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.11.1\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 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\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 "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\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 "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_opener.py", line 8, in open  
return dcm.open()  
^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom.py", line 47, in open  
patient.render()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 123, in render  
study.open_series_as_models()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 214, in
open_series_as_models  
models = s.to_models(all_opened_models, derived, sgrids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 329, in to_models  
grids = data.to_models(open_models, derived, sgrids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 649, in to_models  
models.extend(open_grids(self.session, originals, name=self.name)[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 3854, in open_grids  
v.update_drawings()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 844, in update_drawings  
self._keep_displayed_data = self.displayed_matrices()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1794, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1277, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1301, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_data\griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_models.py", line 214, in read_matrix  
self.dicom_data.read_matrix(  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 948, in read_matrix  
p = self.read_plane(k, time, channel, rescale=False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 970, in read_plane  
data = d.pixel_array  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 1165, in __getattr__  
return self.data.get(item)  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 829, in get  
return getattr(self, key)  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1955, in pixel_array  
self.convert_pixel_data()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1512, in convert_pixel_data  
self._convert_pixel_data_without_handler()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1599, in
_convert_pixel_data_without_handler  
raise RuntimeError(msg + ', '.join(pkg_msg))  
RuntimeError: The following handlers are available to decode the pixel data
however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg
(req. )  
  
RuntimeError: The following handlers are available to decode the pixel data
however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg
(req. )  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1599, in
_convert_pixel_data_without_handler  
raise RuntimeError(msg + ', '.join(pkg_msg))  
  
See log for complete Python traceback.  
  

> open
> D:/iCloudDrive/HDS_Private_Xchange/Personal_Docs/2025-02_Ges_Sonografie_thromb
> format dicom

Summary of feedback from opening
D:/iCloudDrive/HDS_Private_Xchange/Personal_Docs/2025-02_Ges_Sonografie_thromb  
---  
warning | Merged incoming unique studies with existing patient with same ID  
note | Pydicom could not read invalid or non-DICOM file AUT573373.202502030881.zip; skipping.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.11.1\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 1.11.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1420, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\medical_toolbar\\__init__.py", line 36, in run_provider  
actions.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\medical_toolbar\actions.py", line 29, in run_provider  
open_dicom(session)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\medical_toolbar\actions.py", line 37, in open_dicom  
show_open_folder_dialog(session)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 370, in
show_open_folder_dialog  
_folder_dlg.display(session)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 118, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.11.1\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 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\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 "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\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 "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_opener.py", line 8, in open  
return dcm.open()  
^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom.py", line 47, in open  
patient.render()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 123, in render  
study.open_series_as_models()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 214, in
open_series_as_models  
models = s.to_models(all_opened_models, derived, sgrids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 329, in to_models  
grids = data.to_models(open_models, derived, sgrids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 649, in to_models  
models.extend(open_grids(self.session, originals, name=self.name)[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 3854, in open_grids  
v.update_drawings()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 844, in update_drawings  
self._keep_displayed_data = self.displayed_matrices()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1794, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1277, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1301, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_data\griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_models.py", line 214, in read_matrix  
self.dicom_data.read_matrix(  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 948, in read_matrix  
p = self.read_plane(k, time, channel, rescale=False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 970, in read_plane  
data = d.pixel_array  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 1165, in __getattr__  
return self.data.get(item)  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 829, in get  
return getattr(self, key)  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1955, in pixel_array  
self.convert_pixel_data()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1512, in convert_pixel_data  
self._convert_pixel_data_without_handler()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1599, in
_convert_pixel_data_without_handler  
raise RuntimeError(msg + ', '.join(pkg_msg))  
RuntimeError: The following handlers are available to decode the pixel data
however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg
(req. )  
  
RuntimeError: The following handlers are available to decode the pixel data
however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg
(req. )  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1599, in
_convert_pixel_data_without_handler  
raise RuntimeError(msg + ', '.join(pkg_msg))  
  
See log for complete Python traceback.  
  

> open
> D:/iCloudDrive/HDS_Private_Xchange/Personal_Docs/2025-02_Ges_Sonografie_thromb/1.2.392.200036.9116.6.33.11522202.2353.20250203123425382.1.875.dcm

Summary of feedback from opening
D:/iCloudDrive/HDS_Private_Xchange/Personal_Docs/2025-02_Ges_Sonografie_thromb/1.2.392.200036.9116.6.33.11522202.2353.20250203123425382.1.875.dcm  
---  
warning | Merged incoming unique studies with existing patient with same ID  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 355, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.11.1\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 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\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 "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\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 "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_opener.py", line 8, in open  
return dcm.open()  
^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom.py", line 47, in open  
patient.render()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 123, in render  
study.open_series_as_models()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 214, in
open_series_as_models  
models = s.to_models(all_opened_models, derived, sgrids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 329, in to_models  
grids = data.to_models(open_models, derived, sgrids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 649, in to_models  
models.extend(open_grids(self.session, originals, name=self.name)[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 3854, in open_grids  
v.update_drawings()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 844, in update_drawings  
self._keep_displayed_data = self.displayed_matrices()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1794, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1277, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1301, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_data\griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_models.py", line 214, in read_matrix  
self.dicom_data.read_matrix(  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 948, in read_matrix  
p = self.read_plane(k, time, channel, rescale=False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 970, in read_plane  
data = d.pixel_array  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\dicom\dicom_hierarchy.py", line 1165, in __getattr__  
return self.data.get(item)  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 829, in get  
return getattr(self, key)  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1955, in pixel_array  
self.convert_pixel_data()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1512, in convert_pixel_data  
self._convert_pixel_data_without_handler()  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1599, in
_convert_pixel_data_without_handler  
raise RuntimeError(msg + ', '.join(pkg_msg))  
RuntimeError: The following handlers are available to decode the pixel data
however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg
(req. )  
  
RuntimeError: The following handlers are available to decode the pixel data
however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg
(req. )  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\pydicom\dataset.py", line 1599, in
_convert_pixel_data_without_handler  
raise RuntimeError(msg + ', '.join(pkg_msg))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 452.69
OpenGL renderer: Quadro T1000 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: en_AT.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Fury 15 G7 Mobile Workstation
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 85,660,639,232
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-GB

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
    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: 2026.1.4
    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
    comtypes: 1.4.11
    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
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    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
    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
    pywin32: 311
    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
    tzdata: 2025.3
    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
    WMI: 1.5.1
    yarl: 1.22.0

[Eric Pettersen]

Reported by Harald Dauwa-Stummer

[Zach Pearson]

pip install gdcm in the ChimeraX command line for an immediate fix, but it would be good to tell the user that instead of issuing that traceback