Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6501 closed defect (can't reproduce)

Session restore problem: Chain ID cannot be the empty string

Reported by: i.ihnatenko@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
cxs file which was generated with ChimeraX 0.91 (2019-06-01) cannot be opened with ChimeraX 1.3 (2021-12-08) but is still functioning in the ChimeraX 0.91 version.

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Irina/PowerFolders/Arbeit/Grundlegende pdb-files/Docking-
> Ergebnisse/GOLDDOCK20220327_2constraints-a-la-
> Orban/Ergebnisse/ChimeraX_working_20220329.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 725, in restore  
obj = sm.restore_snapshot(self, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1346, in restore_snapshot  
s.set_state_from_snapshot(session, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1353, in set_state_from_snapshot  
Structure.set_state_from_snapshot(self, session, data['structure state'])  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 214, in set_state_from_snapshot  
StructureData.set_state_from_snapshot(self, session, data['structure state'])  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1799, in set_state_from_snapshot  
f(self._c_pointer, data['version'], tuple(data['ints']),
tuple(data['floats']), tuple(data['misc']))  
TypeError: Chain ID cannot be the empty string  
  
opened ChimeraX session  




OpenGL version: 3.3.0 - Build 27.20.100.8854
OpenGL renderer: Intel(R) HD Graphics 510
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 5050
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 8,446,881,792
MaxProcessMemory: 137,438,953,344
CPU: 2 Intel(R) Pentium(R) CPU G4400 @ 3.30GHz
OSLanguage: de-DE
Locale: ('de_DE', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (6)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Session restore problem: Chain ID cannot be the empty string

comment:2 by Eric Pettersen, 4 years ago

Status: accepted → feedback

Hi Irina,

Thanks for reporting this problem. I have made a change which I believe will allow your session to open. It is difficult to test myself since I don't have a session that old with blank chain IDs. So please try tomorrow's daily build and see if your session opens. If it still does not, sending me the session file would really help me test any further fixes I would need to make...

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by i.ihnatenko@…, 4 years ago 

Dear Eric,

Thank you for your swift reply. Let me quickly tell you what I actually 
planned to do:

I wanted to visualise the docking results (130 solutions/conformations 
in one mol2 file) in a protein (also mol2 file) and saved them as the 
cdx project. To evade the problem with the cdx file, I did not start 
with the already existing cdx file, but tried to load the protein mol2 
file and the ligands mol2 file directly into ChimeraX 1.3 (or the daily 
build version 1.4.dev202203301843 (2022-03-30)). A problem still 
occurred: the protein was loading fine, but the ligand conformations 
could not be opened, and I got this message from ChimeraX as a reply: 
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xfc in position 
474: invalid start byte

I did find a workaround though. I opened the mol2 file with the ChimeraX 
0.91 version and just saved a copy as a pdb file. This file was opening 
fine with the two latest ChimeraX versions and, apparently, no 
information got lost (according to my visual inspection) apart from the 
names of the different ligands/conformations (in 'models').

I am sorry I cannot send you the project file as we have not published 
the structures yet. So I performed another GOLD docking run today with 
the same settings but generic structures. In this case I couldn't 
reproduce the error and the two mol2 files of the protein and the 
ligands were opening fine with the two latest ChimeraX versions. Still, 
thank you so much for your time.

Cheers,

Irina


Am 30.03.2022 um 20:05 schrieb ChimeraX:

comment:4 by Eric Pettersen, 4 years ago

Resolution: → can't reproduce
Status: feedback → closed

Hi Irina,

I'm glad you found something that works for you. What I had hoped is that you could try opening that old session file (ChimeraX_working_20220329.cxs) in the current daily build to see if the change I made allows it to be opened. But since you found something that works for you, it is slightly moot now. :-)

--Eric

in reply to:  5 ; comment:5 by i.ihnatenko@…, 4 years ago 

Dear Eric,

I also tried opening the old session file in your latest daily build, but unfortunately it did not open properly. I wrote this solely in case you were curious whether it worked.

Cheers,

Irina


_
Irina Ihnatenko
Wissenschaftliche Mitarbeiterin | scientific staff

Technische Universität Braunschweig
Institut für Medizinische und Pharmazeutische Chemie<https://www.tu-braunschweig.de/pharmchem> (IMPC) | Institute of Medicinal and Pharmaceutical Chemistry
R407, Beethovenstr 55, 38106 Braunschweig, Germany

Tel +49 531 391 2748
Mail i.ihnatenko@tu-braunschweig.de

________________________________
Von: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Gesendet: Donnerstag, 31. März 2022 23:24:40
Cc: Ihnatenko, Irina; pett@cgl.ucsf.edu
Betreff: Re: [ChimeraX] #6501: Session restore problem: Chain ID cannot be the empty string

#6501: Session restore problem: Chain ID cannot be the empty string
--------------------------------------+--------------------
          Reporter:  i.ihnatenko@…    |      Owner:  pett
              Type:  defect           |     Status:  closed
          Priority:  normal           |  Milestone:
         Component:  Sessions         |    Version:
        Resolution:  can't reproduce  |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+--------------------
Changes (by pett):

 * status:  feedback => closed
 * resolution:   => can't reproduce


Comment:

 Hi Irina,
         I'm glad you found something that works for you.  What I had hoped
 is that you could try opening that old session file
 (ChimeraX_working_20220329.cxs) in the current daily build to see if the
 change I made allows it to be opened.  But since you found something that
 works for you, it is slightly moot now. :-)

 --Eric

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6501#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:6 by Eric Pettersen, 4 years ago

Thanks for letting me know.

--Eric

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