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Opened 4 hours ago
#20086 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
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
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