Opened 4 months ago

Closed 4 months ago

Last modified 4 months ago

#18045 closed defect (limitation)

Problem reading .cmm file

Reported by: horvath.peter.3@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.14.9-200.fc41.x86_64-x86_64-with-glibc2.40
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
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 /home/user/CryoEM/E3_wt_sharp.mrc format mrc

Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at
level 0.136, step 1, values float32  

> open "/home/user/CryoEM/homology models/test1.pdb"

test1.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) e3_wt [more info...]  
  
Chain information for test1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in test1.pdb #2  
---  
FAD — (FAD)  
  

> close session

> open /home/user/CryoEM/E3_wt_sharp.mrc format mrc

Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at
level 0.136, step 1, values float32  

> open "/home/user/CryoEM/homology models/test2.cif"

Chain information for test2.cif #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> volume #1 level 0.241

> close session

> open /home/user/CryoEM/E3_wt_sharp.mrc format mrc

Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at
level 0.136, step 1, values float32  

> open "/home/user/CryoEM/homology models/test3.mol2"

Chain information for E3_WT_atomic_model_aligned.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Opened test3.mol2 containing 1 structure (7195 atoms, 7315 bonds)  

> close session

> open /home/user/CryoEM/E3_wt_sharp.mrc format mrc

Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at
level 0.136, step 1, values float32  

> open "/home/user/CryoEM/homology models/test4.dcd"

No atomic models open to read the coordinates into!  

> close session

> open /home/user/CryoEM/E3_wt_sharp.mrc format mrc

Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at
level 0.136, step 1, values float32  

> open "/home/user/CryoEM/homology models/test5.cmm"

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/expatreader.py", line
217, in feed  
self._parser.Parse(data, isFinal)  
xml.parsers.expat.ExpatError: no element found: line 1, column 0  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/markers/__init__.py", line 62, in open  
return cmmfiles.read_cmm(session, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/markers/cmmfiles.py", line 7, in read_cmm  
msets = load_markerset_xml(session, f)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/markers/cmmfiles.py", line 181, in load_markerset_xml  
xml_parser.parse(input)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/expatreader.py", line
111, in parse  
xmlreader.IncrementalParser.parse(self, source)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/xmlreader.py", line
127, in parse  
self.close()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/expatreader.py", line
240, in close  
self.feed(b"", isFinal=True)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/expatreader.py", line
221, in feed  
self._err_handler.fatalError(exc)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/handler.py", line 38,
in fatalError  
raise exception  
xml.sax._exceptions.SAXParseException: /home/user/CryoEM/homology
models/test5.cmm:1:0: no element found  
  
xml.sax._exceptions.SAXParseException: /home/user/CryoEM/homology
models/test5.cmm:1:0: no element found  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/handler.py", line 38,
in fatalError  
raise exception  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 575.57.08
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasmax11
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:0
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G10DK_G10DK
OS: Fedora Linux 41
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 AMD Ryzen 5 5600X 6-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       9.8Gi       3.3Gi       261Mi        18Gi        21Gi
	Swap:          8.0Gi       764Ki       8.0Gi

Graphics:
	13:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106 [GeForce RTX 3060 Lite Hash Rate] [10de:2504] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:8811]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    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-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (3)

comment:1 by pett, 4 months ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem reading .cmm file

Reported by Peter Horvath

comment:2 by Tom Goddard, 4 months ago

Resolution: → limitation
Status: assigned → closed

This error is from opening a ChimeraX .cmm file that is empty. An empty files is not a legal marker file. Unfortunately ChimeraX 1.9 and earlier would write an empty file if you asked it to save markers and there were none to save. That bug was fixed in ChimeraX 1.10 so it will no longer write empty marker files and trying to save such a file will warn that there are no markers, and not write the file.

comment:3 by horvath.peter.3@…, 4 months ago 

Hi Tom,
I’m having an issue in ChimeraX and would appreciate your help.
I aligned an atomic model with a cryo-EM map and would like to save the atomic model in its aligned position, so that when I reopen both the map and the model later, they appear properly aligned.
I tried using the GUI to save the transformed atomic model in different formats, but when I reopened the files, the alignment was lost.
I also tried using the save command, but encountered the same issue — the model was saved in its original, unaligned coordinates.
Finally, I attempted to save the session as a .cxs file and open it in Chimera, but Chimera cannot open .cxs session files from ChimeraX.
Could you please tell me exactly what I need to do to save the atomic model with its current (transformed) coordinates so that it stays aligned with the map when reloaded?
Thank you very much for your help.
Wishing you a great day,
Peter


________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, June 23, 2025 8:41 PM
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Horváth Péter <horvath.peter.3@pte.hu>
Subject: Re: [ChimeraX] #18045: Problem reading .cmm file

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#18045: Problem reading .cmm file
----------------------------------------+-------------------------
          Reporter:  horvath.peter.3@…  |      Owner:  Tom Goddard
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Input/Output       |    Version:
        Resolution:  limitation         |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
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Changes (by Tom Goddard):

 * resolution:   => limitation
 * status:  assigned => closed

Comment:

 This error is from opening a ChimeraX .cmm file that is empty.  An empty
 files is not a legal marker file.  Unfortunately ChimeraX 1.9 and earlier
 would write an empty file if you asked it to save markers and there were
 none to save.  That bug was fixed in ChimeraX 1.10 so it will no longer
 write empty marker files and trying to save such a file will warn that
 there are no markers, and not write the file.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18045#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

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