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Opened 18 hours ago
#19326 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-10-10.0.26100
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
unable to view any residues. there is a blank white background - the background doesnt change to black when chosen. I can still see individual labels of residues when the mouse hovers over them.
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\alyou\Documents\Telomerase Project\Materials And
> Methods\Molecular Dynamics\modified-hTERT for MD .cxs" format session
Log from Sat Mar 1 02:56:45 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/alyou/Documents/Telomerase Project/Materials And
> Methods/Molecular Dynamics/From
> Adwaith/WT/WT/7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb"
Summary of feedback from opening C:/Users/alyou/Documents/Telomerase
Project/Materials And Methods/Molecular Dynamics/From
Adwaith/WT/WT/7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb
---
warnings | Start residue of secondary structure not found: HELIX 9 9 LYS A 329 LEU A 332 1 4
Start residue of secondary structure not found: HELIX 10 10 PHE A 345 LEU A
350 1 6
Start residue of secondary structure not found: HELIX 11 11 SER A 353 LEU A
366 1 14
Start residue of secondary structure not found: HELIX 12 12 PRO A 383 GLN A
402 1 20
Start residue of secondary structure not found: HELIX 13 13 PRO A 404 CYS A
413 1 10
67 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (982 )
7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb
title:
Cryo-em structure of human telomerase-DNA-TPP1-POT1 complex (with POT1 side
chains) [more info...]
Chain information for
7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb
#1
---
Chain | Description | UniProt
A | telomerase reverse transcriptase | TERT_HUMAN 1-1132
B | RNA (256-mer) |
C | No description available |
D | No description available |
E | No description available |
L | histone H2A | B2R5B3_HUMAN 1-130
M | histone H2B | B4DR52_HUMAN 1-166
N | telomeric DNA |
O | adrenocortical dysplasia protein homolog |
P | protection of telomeres protein 1 | POTE1_HUMAN 1-634
Q | No description available |
R | No description available |
> sequence chain #1/A
Alignment identifier is 1/A
> select clear
> select /A
1327 atoms, 1359 bonds, 173 residues, 1 model selected
> select clear
[Repeated 2 time(s)]
> select /A
1327 atoms, 1359 bonds, 173 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> sequence chain #1/B
Alignment identifier is 1/B
> select clear
> select /B
3696 atoms, 4121 bonds, 175 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> nucleotides sel tube/slab shape box
> show sel atoms
> color sel yellow
> sequence chain #1/C
Alignment identifier is 1/C
> select clear
> select /C
2041 atoms, 2277 bonds, 96 residues, 1 model selected
> nucleotides sel tube/slab shape box
> show sel cartoons
> color sel yellow
> sequence chain #1/D
Alignment identifier is 1/D
> select /D:417
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /D
784 atoms, 810 bonds, 96 residues, 1 model selected
> hide sel atoms
> show sel cartoons
[Repeated 2 time(s)]
> sequence chain #1/E
Alignment identifier is 1/E
> select /E:1132
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /E:499-1132
5091 atoms, 5205 bonds, 634 residues, 1 model selected
> select /E:1132
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /E
5558 atoms, 5686 bonds, 689 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> sequence chain #1/L
Alignment identifier is 1/L
> show sel cartoons
> hide sel atoms
> select clear
> select /L
643 atoms, 650 bonds, 82 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> sequence chain #1/M
Alignment identifier is 1/M
> select /M:106-125
147 atoms, 148 bonds, 20 residues, 1 model selected
> select /M
699 atoms, 710 bonds, 90 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> sequence chain #1/N
Alignment identifier is 1/N
> select clear
> select /N
207 atoms, 232 bonds, 10 residues, 1 model selected
> nucleotides sel tube/slab shape box
> show sel cartoons
> color sel lime
> sequence chain #1/O
Alignment identifier is 1/O
> select clear
> select /O
1143 atoms, 1163 bonds, 149 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> sequence chain #1/P
Alignment identifier is 1/P
> select clear
> select /P
948 atoms, 971 bonds, 120 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> sequence chain #1/Q
Alignment identifier is 1/Q
> select /Q:299
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /Q
1187 atoms, 1210 bonds, 149 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> sequence chain #1/R
Alignment identifier is 1/R
> select /R:30
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /R
251 atoms, 282 bonds, 12 residues, 1 model selected
> nucleotides sel tube/slab shape box
> show sel cartoons
> color sel lime
> sequence chain #1/A
Alignment identifier is 1/A
> select clear
[Repeated 2 time(s)]
> select /A
1327 atoms, 1359 bonds, 173 residues, 1 model selected
> ui tool show "Model Loops"
> sequence chain #1/C
Alignment identifier is 1/C
> sequence chain #1/D
Alignment identifier is 1/D
> select /D:417
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /D
784 atoms, 810 bonds, 96 residues, 1 model selected
> ui tool show "Model Loops"
> modeller refine 1/D:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> select protein
12289 atoms, 12559 bonds, 1548 residues, 1 model selected
> ui tool show "Model Loops"
> ui tool show AlphaFold
> ui tool show "Similar Structures"
> foldseek /A
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.9\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 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search
FoldseekWebQuery(session, chain, database=database,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__
mmcif_string = _mmcif_as_string(chain)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 284, in
_mmcif_as_string
write_mmcif(chain.structure.session, f.name, models = [structure])
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\alyou\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_t_vxbd_9.cif'
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\alyou\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_t_vxbd_9.cif'
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif
See log for complete Python traceback.
> sequence search /A
Found 45 similar structures to
7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb
#1/A in pdb database using mmseqs2, name mm1
> sequence search /A
Found 45 similar structures to
7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb
#1/A in pdb database using mmseqs2, name mm2
> ui tool show "Show Sequence Viewer"
> ui tool show "Build Structure"
> ui tool show "Model Loops"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 347, in _update_sequence_menus
row_info.fieldItem.widget().destroy()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\widgets.py", line 104, in destroy
self.alignment.remove_observer(self)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 711, in remove_observer
self.observers.remove(observer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 711, in remove_observer
self.observers.remove(observer)
See log for complete Python traceback.
> mlp sel
Map values for surface
"7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb_A
SES surface": minimum -25.64, mean -2.206, maximum 23.45
Map values for surface
"7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb_D
SES surface": minimum -26.58, mean -2.199, maximum 24.02
Map values for surface
"7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb_E
SES surface": minimum -29.82, mean -2.987, maximum 26.57
Map values for surface
"7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb_L
SES surface": minimum -27.9, mean -2.575, maximum 22.51
Map values for surface
"7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb_M
SES surface": minimum -23.84, mean -2.815, maximum 21.05
Map values for surface
"7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb_O
SES surface": minimum -25.58, mean -4.805, maximum 24.08
Map values for surface
"7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb_P
SES surface": minimum -27.49, mean -2.936, maximum 23.08
Map values for surface
"7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb_Q
SES surface": minimum -27.6, mean -4.902, maximum 20.8
To also show corresponding color key, enter the above mlp command and add key
true
> color sel bychain
> lighting flat
> lighting simple
> lighting full
> set bgColor white
> select /A
1327 atoms, 1359 bonds, 173 residues, 1 model selected
> select /O
1143 atoms, 1163 bonds, 149 residues, 1 model selected
> color (#!1 & sel) hot pink
> select /A
1327 atoms, 1359 bonds, 173 residues, 1 model selected
> color (#!1 & sel) cyan
> select /Q
1187 atoms, 1210 bonds, 149 residues, 1 model selected
> color (#!1 & sel) cornflower blue
> select /P
948 atoms, 971 bonds, 120 residues, 1 model selected
> color (#!1 & sel) blue
> color (#!1 & sel) medium blue
> select /R
251 atoms, 282 bonds, 12 residues, 1 model selected
> select /D
784 atoms, 810 bonds, 96 residues, 1 model selected
> select /C
2041 atoms, 2277 bonds, 96 residues, 1 model selected
> select /D
784 atoms, 810 bonds, 96 residues, 1 model selected
> select /E
5558 atoms, 5686 bonds, 689 residues, 1 model selected
> color (#!1 & sel) orange red
> select /D
784 atoms, 810 bonds, 96 residues, 1 model selected
> color (#!1 & sel) orange
> cd "C:/Users/alyou/Documents/Telomerase Project/Materials And
> Methods/Molecular Dynamics"
Current working directory is: C:\Users\alyou\Documents\Telomerase
Project\Materials And Methods\Molecular Dynamics
> save "C:/Users/alyou/Documents/Telomerase Project/Materials And
> Methods/Molecular Dynamics/modified-hTERT for MD .cxs"
——— End of log from Sat Mar 1 02:56:45 2025 ———
> view name session-start
opened ChimeraX session
> hide #!1 models
> show #!1 models
> show target m
> log metadata #1
No models had metadata
> log chains #1
Chain information for
7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb
#1
---
Chain | Description | UniProt
A | telomerase reverse transcriptase | TERT_HUMAN 1-1132
B | RNA (256-mer) |
C | No description available |
D | No description available |
E | No description available |
L | histone H2A | B2R5B3_HUMAN 1-130
M | histone H2B | B4DR52_HUMAN 1-166
N | telomeric DNA |
O | adrenocortical dysplasia protein homolog |
P | protection of telomeres protein 1 | POTE1_HUMAN 1-634
Q | No description available |
R | No description available |
> log metadata #1
No models had metadata
> log chains #1
Chain information for
7qxs_chain_filled_split_small_protein_modelled_split_final_used_for_final_run.pdb
#1
---
Chain | Description | UniProt
A | telomerase reverse transcriptase | TERT_HUMAN 1-1132
B | RNA (256-mer) |
C | No description available |
D | No description available |
E | No description available |
L | histone H2A | B2R5B3_HUMAN 1-130
M | histone H2B | B4DR52_HUMAN 1-166
N | telomeric DNA |
O | adrenocortical dysplasia protein homolog |
P | protection of telomeres protein 1 | POTE1_HUMAN 1-634
Q | No description available |
R | No description available |
OpenGL version: 3.3.0 Core Profile Context 25.10.2.250822
OpenGL renderer: AMD Radeon RX 7700S
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_CA.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming A16 FA617NT_FA617NT
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,369,319,936
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 7735HS with Radeon Graphics
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2025.6.15
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-cuda-cupti-cu12: 12.9.79
nvidia-cuda-nvcc-cu12: 12.9.86
nvidia-cuda-nvrtc-cu12: 12.9.86
nvidia-cuda-runtime-cu12: 12.9.79
nvidia-cufft-cu12: 11.4.1.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
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