Opened 5 years ago

Closed 5 years ago

#4362 closed defect (fixed)

Segger: thrD is None

Reported by: bcook@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: gregdp@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
I was trying to segement a processed tomogram and recieved this error: 
'TypeError: must be real number, not NoneType

File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )

See log for complete Python traceback.'

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 "C:/Users/mherzik/Desktop/Brian/Mitos/Tomo5 Test 3.mrc"

Summary of feedback from opening C:/Users/mherzik/Desktop/Brian/Mitos/Tomo5
Test 3.mrc  
---  
note | C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5 Test 3.mrc: invalid cell
angles 0,0,0 must be between 0 and 180.  
  
Opened Tomo5 Test 3.mrc, grid size 960,928,375, pixel 1, shown at step 1,
values float32  

> ui tool show "Segment Map"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  

> select #1

2 models selected  

> ~select #1

Nothing selected  

> select #1

2 models selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  

> close session

> open "C:/Users/mherzik/Desktop/Brian/Mitos/Tomo5 Test.mrc"

Summary of feedback from opening C:/Users/mherzik/Desktop/Brian/Mitos/Tomo5
Test.mrc  
---  
note | C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5 Test.mrc: invalid cell
angles 0,0,0 must be between 0 and 180.  
  
Opened Tomo5 Test.mrc, grid size 960,928,375, pixel 1, shown at step 1, values
float32  

> ui tool show "Segment Map"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  

> select #1

2 models selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  

> volume #1 level 0,0 level 16.71,0.8 level 43.6,1

> close session

> open "C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5 Test 3.mrc" format mrc

Summary of feedback from opening C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5
Test 3.mrc  
---  
note | C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5 Test 3.mrc: invalid cell
angles 0,0,0 must be between 0 and 180.  
  
Opened Tomo5 Test 3.mrc, grid size 960,928,375, pixel 1, shown at step 1,
values float32  

> ui tool show "Segment Map"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  

> hide #!1 models

> show #!1 models

> select #1

2 models selected  

> ui tool show "Volume Viewer"

No segmentation chosen  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  

> close session

> open "C:/Users/mherzik/Desktop/Brian/Mitos/Tomo5 Test 2.mrc"

Summary of feedback from opening C:/Users/mherzik/Desktop/Brian/Mitos/Tomo5
Test 2.mrc  
---  
note | C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5 Test 2.mrc: invalid cell
angles 0,0,0 must be between 0 and 180.  
  
Opened Tomo5 Test 2.mrc, grid size 960,928,375, pixel 1, shown at step 1,
values float32  

> ui tool show "Segment Map"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  

> toolshed show

> close session

> open
> C:/Users/mherzik/Desktop/Brian/Mitos/TEM_20190731_DS_017_mDS002_1_TL_L1_2_T05_DW.rec

Opened TEM_20190731_DS_017_mDS002_1_TL_L1_2_T05_DW.rec, grid size 960,928,375,
pixel 17.1,17.1,17.1, shown at step 1, values int8  

> ui tool show "Segment Map"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  

> close session

> open "C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5 Test 3.mrc" format mrc

Summary of feedback from opening C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5
Test 3.mrc  
---  
note | C:\Users\mherzik\Desktop\Brian\Mitos\Tomo5 Test 3.mrc: invalid cell
angles 0,0,0 must be between 0 and 180.  
  
Opened Tomo5 Test 3.mrc, grid size 960,928,375, pixel 1, shown at step 1,
values float32  

> ui tool show "Segment Map"

No segmentation chosen  
No segmentation selected  
No segmentation chosen  
No segmentation selected  
No segmentation chosen  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 399, in _segment  
self.Segment()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2133, in Segment  
smod = self.SegmentAndGroup(show, group)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
TypeError: must be real number, not NoneType  
  
TypeError: must be real number, not NoneType  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 2149, in SegmentAndGroup  
self.status ( "Segmenting %s, density threshold %f" % (mm.name, thrD) )  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 461.40
OpenGL renderer: TITAN V/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 137,305,980,928
MaxProcessMemory: 137,438,953,344
CPU: 64 AMD Ryzen Threadripper 3970X 32-Core Processor "
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

Change History (3)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segger: thrD is None

Reported by Brian Cook

comment:2 by Tom Goddard, 5 years ago

Cc: gregdp@… added

This Segger bug happens when trying to segment a map that has no surface shown. With your tomogram it probably displays a gray scale image in ChimeraX. Segger uses the threshold level set by the displayed surface and apparently is not checking that there is no displayed surface. To avoid this error use the Volume VIewer panel and choose style "surface" from the menu above the histogram at the far right, and also display the whole volume not just one plane since Segger works on the displayed region -- ctrl click or right click on the histogram and use "Show full region". Alternatively use command "volume #1 region all style surface". Then the you should be able to segment.

Segger was not designed to operate on tomograms -- it was developed for single particle cryoEM. So it is unlikely to give useful results, but you can try.

comment:3 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Made Segger give a warning saying map must have a surface because the surface threshold level is used by the segmentation algorithm.

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