The following bug report has been submitted:
Platform: macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.7.dev202308310222 (2023-08-31 02:22:34 UTC)
Description
Unable to use PDBIMages. I get this error:
pdbimages /Users/prash_mbp/virus width 800 height 800 supersample 3 imageSuffix .png
set bgColor white
set silhouettes false
lighting soft
log settings warningDialog false errorDialog false
Rendering 4 mmCIF files /Users/prash_mbp/virus/6koe.cif No module named 'chimerax.atomic.mmcif' /Users/prash_mbp/virus/5doq.cif No module named 'chimerax.atomic.mmcif' /Users/prash_mbp/virus/6koc.cif No module named 'chimerax.atomic.mmcif' /Users/prash_mbp/virus/6kob.cif No module named 'chimerax.atomic.mmcif'
Log:
UCSF ChimeraX version: 1.7.dev202308310222 (2023-08-31)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed show
> cd
Current working directory is: /Users/prash_mbp
> pdbimages /virus width 800 height 800 supersample 3 imageSuffix .png exclude
> 1m4x.cif,3j3q.cif
> set bgColor white
> set silhouettes false
> lighting soft
> log settings warningDialog false errorDialog false
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/prash_mbp/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/pdb_images/pdbimages.py", line 47, in pdbimages
mmcifs = cif_files(directory, subdirectories, exclude, image_suffix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/prash_mbp/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/pdb_images/pdbimages.py", line 73, in cif_files
files = listdir(directory)
^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/virus'
FileNotFoundError: [Errno 2] No such file or directory: '/virus'
File "/Users/prash_mbp/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/pdb_images/pdbimages.py", line 73, in cif_files
files = listdir(directory)
^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> pdbimages /Users/prash_mbp/virus width 800 height 800 supersample 3
> imageSuffix .png exclude 1m4x.cif,3j3q.cif
> set bgColor white
> set silhouettes false
> lighting soft
> log settings warningDialog false errorDialog false
Rendering 0 mmCIF files
> pdbimages /Users/prash_mbp/virus width 800 height 800 supersample 3
> imageSuffix .png exclude 1m4x.cif,3j3q.cif
> set bgColor white
> set silhouettes false
> lighting soft
> log settings warningDialog false errorDialog false
Rendering 0 mmCIF files
> open "/Users/prash_mbp/Downloads/batch-download-structures-1696949338107
> 2/1cyw-assembly1.cif"
mmCIF parsing error: unexpected data value near line 1
> open /Users/prash_mbp/Downloads/6kob.cif
Summary of feedback from opening /Users/prash_mbp/Downloads/6kob.cif
---
notes | Fetching CCD HEA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/HEA/HEA.cif
Fetching CCD CU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/CU/CU.cif
6kob.cif title:
X-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase
from Bacillus subtilis [more info...]
Chain information for 6kob.cif #1
---
Chain | Description | UniProt
A E | AA3-600 quinol oxidase subunit I | A0A063X8D0_BACIU 1-649
B F | Quinol oxidase subunit 2 | A0A2I7T8S1_BACIU 1-296
C G | AA3-600 quinol oxidase subunit IIII | A0A063X6N5_BACIU 1-204
D H | AA3-600 quinol oxidase subunit IV,Quinol oxidase subunit 4 | QOX4_BACSU
48-124
Non-standard residues in 6kob.cif #1
---
CU — copper (II) ion
HEA — heme-A
MQ7 — menaquinone-7
6kob.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> pdbimages /Users/prash_mbp/virus width 800 height 800 supersample 3
> imageSuffix .png exclude 1m4x.cif,3j3q.cif
> set bgColor white
> set silhouettes false
> lighting soft
> log settings warningDialog false errorDialog false
Rendering 0 mmCIF files
> pdbimages /Users/prash_mbp/virus width 800 height 800 supersample 3
> imageSuffix .png
> set bgColor white
> set silhouettes false
> lighting soft
> log settings warningDialog false errorDialog false
Rendering 0 mmCIF files
> pdbimages /Users/prash_mbp/virus width 800 height 800 supersample 3
> imageSuffix .png
> set bgColor white
> set silhouettes false
> lighting soft
> log settings warningDialog false errorDialog false
Rendering 1 mmCIF files
/Users/prash_mbp/virus/6kob.cif
No module named 'chimerax.atomic.mmcif'
> close session
> pdbimages /Users/prash_mbp/virus width 800 height 800 supersample 3
> imageSuffix .png
> set bgColor white
> set silhouettes false
> lighting soft
> log settings warningDialog false errorDialog false
Rendering 1 mmCIF files
/Users/prash_mbp/virus/6kob.cif
No module named 'chimerax.atomic.mmcif'
> toolshed show
> help help:user
> pdbimages /Users/prash_mbp/virus width 800 height 800 supersample 3
> imageSuffix .png
> set bgColor white
> set silhouettes false
> lighting soft
> log settings warningDialog false errorDialog false
Rendering 4 mmCIF files
/Users/prash_mbp/virus/6koe.cif
No module named 'chimerax.atomic.mmcif'
/Users/prash_mbp/virus/5doq.cif
No module named 'chimerax.atomic.mmcif'
/Users/prash_mbp/virus/6koc.cif
No module named 'chimerax.atomic.mmcif'
/Users/prash_mbp/virus/6kob.cif
No module named 'chimerax.atomic.mmcif'
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK183LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 4 days, 16 hours, 14 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U3421WE:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.47.1
ChimeraX-AtomicLibrary: 10.0.8
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.4
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202308310222
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBImages: 1.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.31.4
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7.post1
decorator: 5.1.1
docutils: 0.19
et-xmlfile: 1.1.0
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.0
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.7
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.5
numpy: 1.25.1
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.1.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
seaborn: 0.12.2
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.2
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed by new PDBImages bundle in Toolshed. Use menu Tools / More tools... or menu Tools / Utilities / Updates to install the new version (1.2).
The old code was changed by Eric in 2020 when he eliminated chimerax.atomic.mmcif in favor of chimerax.mmcif, but the Toolshed bundle never got updated.