Opened 4 years ago

Closed 4 years ago

#5611 closed defect (duplicate)

Segger model added to scene twice

Reported by: mpm896@… 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-4.4.0-201-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Not sure what caused the issue. I segmented a structure using Segger and saved the resulting file as a .cxs. Upon trying to open that .cxs file, I get this error. 

Between then and now, I did not delete or change any of the files, update python, or update ChimeraX.

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/run7_AV_masked_inverse.mrc
> format mrc

Summary of feedback from opening
/ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/run7_AV_masked_inverse.mrc  
---  
note |
/ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/run7_AV_masked_inverse.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened run7_AV_masked_inverse.mrc, grid size 90,90,90, pixel 1, shown at level
5.66, step 1, values float32  

> set bgColor white

> volume #1

> volume #1 style image region 0,0,44,89,89,44 step 1 showOutlineBox true

> close #1

> open
> /ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/run7_AV_inverse.mrc
> format mrc

Summary of feedback from opening
/ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/run7_AV_inverse.mrc  
---  
note |
/ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/run7_AV_inverse.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened run7_AV_inverse.mrc, grid size 90,90,90, pixel 1, shown at level 5.66,
step 1, values float32  

> volume #1 level 2.258

> volume #1 level 0.9838

> volume #1 style image region 0,0,44,89,89,44 step 1 showOutlineBox true

> volume #1 level -1.153,0 level 7.302,0.8 level 7.903,1

> volume #1 level -1.153,0 level 6.66,1 level 7.903,1

> volume #1 level 1.459,0 level 6.66,1 level 7.903,1

> volume #1 level 1.459,0 level 5.776,1 level 7.903,1

> volume #1 level 1.459,0 level 7.478,1 level 7.903,1

> volume #1 level 1.459,0 level 7.478,1 level 8.109,0

> volume #1 level 1.459,0 level 7.478,1 level 7.861,1

> volume #1 level 1.459,0 level 6.484,1 level 7.861,1

> volume #1 level -1.643,0 level 6.484,1 level 7.861,1

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
mpm896@pennmedicine.upenn.edu is subscribed to the ChimeraX announcements list  

> close #1

> open
> /ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/RSA_Segs/Rosette_Crypto_pCC.seg
> format segger

Summary of feedback from opening
/ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/RSA_Segs/Rosette_Crypto_pCC.seg  
---  
notes |
/ChangLab1-hd2/matt/Plasmodium/Rosette/Averages/Rosette_Crypto_invert.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.  
Showing 28 region surfaces  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 629, in customEvent  
func(*args, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer  
cxcmd(session, topic)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 188, in provider_open  
session.models.add(opened_models)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/models.py", line 641, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model Rosette_Crypto_pCC.seg #2 to scene twice  
  
ValueError: Attempted to add model Rosette_Crypto_pCC.seg #2 to scene twice  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/models.py", line 641, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  
Showing Rosette_Crypto_pCC.seg - 28 regions, 28 surfaces  

> close #1

> close #2

> open
> /ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/RSA_Segs/RSA_seg.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore  
obj = sm.restore_snapshot(self, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/segger/regions.py", line 985, in restore_snapshot  
sp = r.make_surface()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/segger/regions.py", line 1189, in make_surface  
tf.transform_points(vertices, in_place = True)  
AttributeError: 'NoneType' object has no attribute 'transform_points'  
  
opened ChimeraX session  

> open
> /ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/RSA_Segs/RSA_seg.cmap

Opened RSA_seg.cmap, grid size 90,90,90, pixel 1, shown at level 5.66, step 1,
values float32  

> volume #1 level -1.623

> close #1

> open
> /ChangLab1-hd2/matt/Plasmodium/Rosette/Dynamo/RhoptryClassAverages_2/RSA_Segs/RSA_seg.cxs
> format session

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore  
obj = sm.restore_snapshot(self, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/segger/regions.py", line 985, in restore_snapshot  
sp = r.make_surface()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/segger/regions.py", line 1189, in make_surface  
tf.transform_points(vertices, in_place = True)  
AttributeError: 'NoneType' object has no attribute 'transform_points'  
  
opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 24 Intel(R) Xeon(R) Gold 6136 CPU @ 3.00GHz
Cache Size: 25344 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        5.4G         10G        662M         46G         55G
	Swap:            0B          0B          0B

Graphics:
	17:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)	
	Subsystem: Dell Device [1028:11a3]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
File attachment: RSA_seg.cxs

RSA_seg.cxs​

Attachments (1)

RSA_seg.cxs​ (3.1 MB ) - added by mpm896@… 4 years ago.
Added by email2trac

Change History (3)

by mpm896@…, 4 years ago

Attachment: RSA_seg.cxs​ added

Added by email2trac

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segger model added to scene twice

Reported by Matthew Martinez

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

This ChimeraX Segger bug was fixed over a year ago (bug #3778). You will not see it if you update to current ChimeraX.

Note: See TracTickets for help on using tickets.