Segger: 'MainWindow' object has no attribute 'save_dialog'

[tolung.bio@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 0.93 (2020-04-03)
Description
Tried saving a segmentation result (137 regions) from the Segment Map window

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:\\\OneDrive\\\OneDrive - University of
> Wollongong\\\Shared\\\GTL_Shared\\\TN\\\Manuscripts\\\Red Beta Structure
> Paper\\\Models\\\beta177_refined_nucleic_260321.pdb"

Summary of feedback from opening D:\\\OneDrive\\\OneDrive - University of
Wollongong\\\Shared\\\GTL_Shared\\\TN\\\Manuscripts\\\Red Beta Structure
Paper\\\Models\\\beta177_refined_nucleic_260321.pdb  
---  
warning | Ignored bad PDB record found on line 3113  
END  
  
Chain information for beta177_refined_nucleic_260321.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hbonds

137 hydrogen bonds found  

> open "D:/OneDrive/OneDrive - University of
> Wollongong/Shared/GTL_Shared/TN/Manuscripts/Red Beta Structure
> Paper/Maps/J195/cryosparc_P8_J195_map_locres.mrc"

Opened cryosparc_P8_J195_map_locres.mrc, grid size 448,448,448, pixel 0.84,
shown at level 7.21, step 2, values float32  

> volume #2 level 6.365

> open "D:/OneDrive/OneDrive - University of
> Wollongong/Shared/GTL_Shared/TN/Manuscripts/Red Beta Structure
> Paper/Maps/J195/cryosparc_P8_J195_map_half_A.mrc"

Opened cryosparc_P8_J195_map_half_A.mrc, grid size 448,448,448, pixel 0.84,
shown at level 0.393, step 2, values float32  

> volume #2 step 1

> volume #2 color #ffffb201

> volume #2 color #ffffb20a

> volume #2 color #ffffb264

> toolshed show "Side View"

> show atoms

> select H

1351 atoms, 1 model selected  

> hide sel target a

> select clear

> open2 "D:/OneDrive/OneDrive - University of
> Wollongong/Shared/GTL_Shared/TN/Manuscripts/Red Beta Structure
> Paper/Maps/J195/cryosparc_P8_J195_mask_refine.mrc"

Opened cryosparc_P8_J195_mask_refine.mrc, grid size 448,448,448, pixel 0.84,
shown at level 1, step 2, values float32  

> open2 "D:/OneDrive/OneDrive - University of
> Wollongong/Shared/GTL_Shared/TN/Manuscripts/Red Beta Structure
> Paper/Maps/J195/cryosparc_P8_J195_map_half_A.mrc"

Opened cryosparc_P8_J195_map_half_A.mrc, grid size 448,448,448, pixel 0.84,
shown at level 0.393, step 2, values float32  

> volume #2 step 1

> volume #2 color #b2b2ff37

> volume #2 color #b2b2ff05

> volume #2 color #b2b2ff01

> volume #2 color #b2b2ff0a

> volume #2 color #b2b2ff64

> volume #2 color #b2b2ff0a

> volume #2 color #b2b2ff01

> volume #2 color #b2b2ff05

> volume #2 color #b2b2ff32

> volume #2 color #b2b2ff01

> volume #2 color #b2b2ff0a

> volume #2 color #b2b2ff64

> volume #2 level 0.3229

> surface dust #2 size 2

> surface dust #2 size 100

> surface dust #2 size 50

> surface dust #2 size 25

> volume #2 level 0.253

> toolshed show "Segment Map"

Segmenting cryosparc_P8_J195_map_half_A.mrc, density threshold 0.253022  
Showing cryosparc_P8_J195_map_half_A.seg - 0 regions, 0 surfaces  
Only showing 150 of 5960 regions.  
Showing 150 of 5960 region surfaces  
2117260 watershed regions, grouped to 5960 regions  

> hide #!3 models

> show #!3 models

> hide #!2 models

> close #3

> open2 "D:/OneDrive/OneDrive - University of
> Wollongong/Shared/GTL_Shared/TN/Manuscripts/Red Beta Structure
> Paper/Maps/J193/cryosparc_P8_J193_map_sharp.mrc"

Opened cryosparc_P8_J193_map_sharp.mrc, grid size 448,448,448, pixel 0.84,
shown at level 0.322, step 2, values float32  
Segmenting cryosparc_P8_J195_map_half_A.mrc, density threshold 0.253022  
Showing cryosparc_P8_J195_map_half_A.seg - 0 regions, 0 surfaces  
Only showing 150 of 5960 regions.  
Showing 150 of 5960 region surfaces  
2117260 watershed regions, grouped to 5960 regions  

> close #4

Segmenting cryosparc_P8_J193_map_sharp.mrc, density threshold 0.322070  
Showing cryosparc_P8_J193_map_sharp.seg - 0 regions, 0 surfaces  
Only showing 150 of 1216 regions.  
Showing 150 of 1216 region surfaces  
19890 watershed regions, grouped to 1216 regions  
Segmenting cryosparc_P8_J193_map_sharp.mrc, density threshold 0.322070  
Showing cryosparc_P8_J193_map_sharp.seg - 0 regions, 0 surfaces  
Only showing 500 of 1216 regions.  
Showing 500 of 1216 region surfaces  
19890 watershed regions, grouped to 1216 regions  

> volume #3 level 0.2356

Segmenting cryosparc_P8_J193_map_sharp.mrc, density threshold 0.235575  
Showing cryosparc_P8_J193_map_sharp.seg - 0 regions, 0 surfaces  
Only showing 1200 of 1359 regions.  
Showing 1200 of 1359 region surfaces  
23628 watershed regions, grouped to 1359 regions  
Smoothing and grouping, standard deviation 5 voxels  
Showing 946 region surfaces  
Got 946 regions after smoothing 5 voxels.  
Smoothing and grouping, standard deviation 6 voxels  
Showing 376 region surfaces  
Got 376 regions after smoothing 6 voxels.  
Smoothing and grouping, standard deviation 7 voxels  
Showing 223 region surfaces  
Got 223 regions after smoothing 7 voxels.  

> hide #!4 models

> hide #!3 models

> show #!4 models

> transparency #4 50

Smoothing and grouping, standard deviation 8 voxels  
Showing 137 region surfaces  
Got 137 regions after smoothing 8 voxels.  

> transparency #4 0

> transparency #4 50

> hide #!1 models

> show #!1 models

> hide #!4 models

> show #!4 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1156, in SaveSegmentation  
self.SaveSegmentationAs()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 461.92
OpenGL renderer: GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B45
OS: Microsoft Windows 10 Education (Build 19042)
Memory: 34,260,611,072
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz"

[pett]

Reported by Gokhan Tolun

[Tom Goddard]

This Segger bug was fixed long ago. You are using ChimeraX 0.93 which is a year old. Suggest updating to ChimeraX 1.1 or to the ChimeraX daily build.