id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4405	self._positions is None	m-schmid@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Opened a .cxs file

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

> open X:/TOXOPLASMA/CONOID_HEIGHT/T22_markers.cxs

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1537, in _tool_window_show  
self._add_tool_panel(tool_window)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1545, in _add_tool_panel  
p = Panel(tool_window, self._ui_model, self, add_titlebar = not is_toolbar)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1911, in __init__  
drawing_parent.add_drawing(d)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py"", line 305, in add_drawing  
if self.display:  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py"", line 355, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger ""tool window show"":  
TypeError: object of type 'NoneType' has no len()  
  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py"", line 355, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1537, in _tool_window_show  
self._add_tool_panel(tool_window)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1545, in _add_tool_panel  
p = Panel(tool_window, self._ui_model, self, add_titlebar = not is_toolbar)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1911, in __init__  
drawing_parent.add_drawing(d)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py"", line 305, in add_drawing  
if self.display:  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py"", line 355, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger ""tool window show"":  
TypeError: object of type 'NoneType' has no len()  
  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py"", line 355, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Log from Wed Mar 24 14:32:53 2021 Startup Messages  
---  
note | available bundle cache was for a different toolshed  
  
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 X:/TOXOPLASMA/CONOID_HEIGHT/T23-axy150u8.hdf

Opened T23-axy150u8.hdf, grid size 928,960,420, pixel 14.2, shown at step 1,
values uint8  

> volume #1 region 0,0,0,927,959,419 step 4

> volume #1 region 0,0,0,927,959,419 step 1 colorMode opaque8 showOutlineBox
> true imageMode ""box faces""

> volume #1

> volume #1 level 86

> volume #1 change image level 79,0 level 89.99,0.8 level 180,1

> surface dust #1 size 200

> color height #1 center 0,0,0 axis z palette rainbow

> vr nearClipDistance 0.5

started SteamVR rendering  
VR mode mark point  

> marker #2 position 5548,5882,-381.4 color yellow radius 1

VR mode resize markers  

> marker change #2 radius 100

> vr false

> hide #!1 models

> show #!1 models

> vr true

started SteamVR rendering  

> marker #2 position 4431,5961,-368.5 color yellow radius 100

> marker #2 position 4437,5993,-427.6 color yellow radius 100

> marker #2 position 3839,8375,2723 color yellow radius 100

> marker #2 position 4561,6188,2537 color yellow radius 100

> marker #2 position 4302,8658,2725 color yellow radius 100

> marker #2 position 5229,6375,2421 color yellow radius 100

> marker #2 position 4754,8946,2834 color yellow radius 100

> marker #2 position 5986,6881,2389 color yellow radius 100

> marker #2 position 3220,8130,2996 color yellow radius 100

> marker #2 position 3867,6099,2748 color yellow radius 100

> marker #2 position 2572,7752,3442 color yellow radius 100

> marker #2 position 3288,5557,3330 color yellow radius 100

> help marker

> vr false

> turn y 180

> marker delete #2:1

Deleted 1 markers  

> marker delete #2:2

Deleted 1 markers  

> marker delete #2:3

Deleted 1 markers  

> marker link #2:4,5 radius 20 color white

> marker link #2:6,7 radius 20 color white

> marker link #2:88,9 radius 20 color white

marker link command requires exactly 2 markers, got 1  

> marker link #2:8,9 radius 20 color white

> marker link #2:10,11 radius 20 color white

> marker link #2:12,13 radius 20 color white

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> save X:/TOXOPLASMA/CONOID_HEIGHT/T23_markers.cxs

> help distance

> distance #2:4 #2:5

Distance between /M mark 4 M and mark 5 M: 2309.883Å  

> distance #2:6 #2:7

Distance between /M mark 6 M and mark 7 M: 2482.802Å  

> distance #2:8 #2:9

Distance between /M mark 8 M and mark 9 M: 2445.361Å  

> distance #2:10 #2:11

Distance between /M mark 10 M and mark 11 M: 2145.351Å  

> distance #2:12 #2:13

Distance between /M mark 12 M and mark 13 M: 2311.031Å  

> save X:/TOXOPLASMA/CONOID_HEIGHT/T23_markers.cxs

> close session

> open X:/TOXOPLASMA/CONOID_HEIGHT/T22-axy150u8.hdf

Opened T22-axy150u8.hdf, grid size 928,960,357, pixel 14.2,14.2,14.2, shown at
step 1, values uint8  

> volume #1 region 0,0,0,927,959,356 step 4

> volume #1 region 0,0,0,927,959,356 step 1 colorMode opaque8 showOutlineBox
> true imageMode ""box faces""

> volume #1

> color height #1 center 0,0,0 axis z palette rainbow

> volume #1 level 80

> volume #1 change image level 73,0 level 87,0.8 level 123,1

> surface dust #1 size 200

> vr true

started SteamVR rendering  

> marker #2 position 5666,8596,3687 color yellow radius 100

> marker #2 position 5854,5499,3978 color yellow radius 100

> marker #2 position 5208,8547,3554 color yellow radius 100

> marker #2 position 5492,5366,3870 color yellow radius 100

> marker #2 position 4905,8494,3289 color yellow radius 100

> marker #2 position 4737,5595,3660 color yellow radius 100

> marker #2 position 6069,8557,3721 color yellow radius 100

> marker #2 position 6447,5609,3965 color yellow radius 100

> marker #2 position 6781,8562,3363 color yellow radius 100

> marker #2 position 7493,6323,3821 color yellow radius 100

> vr false

> hide #!1 models

> distance #2:1 #2:2

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #2:14 #2:15

Distance between /M mark 14 M and mark 15 M: 3117.036Å  

> distance #2:14 #2:15 radius 20 color white

Distance already exists; modify distance properties with 'distance style'  

> marker link #2:14 #2:15 radius 20 color white

> marker link #2:16 #2:17 radius 20 color white

> marker link #2:18 #2:19 radius 20 color white

> marker link #2:20 #2:21 radius 20 color white

> marker link #2:22 #2:23 radius 20 color white

> distance #2:14 #2:15

Distance already exists; modify distance properties with 'distance style'  

> distance #2:16 #2:17

Distance between /M mark 16 M and mark 17 M: 3209.164Å  

> distance #2:18 #2:19

Distance between /M mark 18 M and mark 19 M: 2927.595Å  

> distance #2:20 #2:21

Distance between /M mark 20 M and mark 21 M: 2981.829Å  

> distance #2:22 #2:23

Distance between /M mark 22 M and mark 23 M: 2394.305Å  

> show #!1 models

> save X:/TOXOPLASMA/CONOID_HEIGHT/T22_markers.cxs

opened ChimeraX session  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 130, in invoke  
return self._func(self._name, data)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1537, in _tool_window_show  
self._add_tool_panel(tool_window)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1545, in _add_tool_panel  
p = Panel(tool_window, self._ui_model, self, add_titlebar = not is_toolbar)  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1911, in __init__  
drawing_parent.add_drawing(d)  
AttributeError: 'NoneType' object has no attribute 'add_drawing'  
  
Error processing trigger ""tool window show"":  
AttributeError: 'NoneType' object has no attribute 'add_drawing'  
  
File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\vive\vr.py"", line 1911, in __init__  
drawing_parent.add_drawing(d)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Microsoft Windows 10 Pro (Build 18363)
Memory: 17,086,476,288
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz""
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: 2.1.1
    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: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 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
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    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+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1

}}}
"	defect	closed	normal		VR		fixed						all	ChimeraX