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Opened 3 years ago
Closed 3 years ago
#7751 closed defect (duplicate)
Segger session save: invalid literal for int
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving session data for 'tools' -> -> 'segment map'
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/jliu/Desktop/Export_appratus/Session/3A.cxs
Opened Bb-EXP-2.7A.mrc as #1, grid size 128,128,128, pixel 2.7, shown at step
1, values float32
Opened Bb-EXP-2.7A_imasked as #4, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #6, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked as #3, grid size 128,128,128, pixel 2.7, shown
at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked as #8, grid size 128,128,128, pixel
2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked as #10, grid size 128,128,128,
pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked as #13, grid size
128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #15, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#17, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2.7A_imasked as #5, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
Opened Bb-EXP-2.7A_imasked as #9, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #7, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #11, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #18, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #19, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #20, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #21, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#22, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#23, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2.7A_imasked as #24, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Log from Tue Oct 4 14:34:08 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/jliu/Desktop/Export_appratus/Session/3B.cxs
Opened Bb-EXP-2.7A.mrc as #1, grid size 128,128,128, pixel 2.7, shown at step
1, values float32
Opened Bb-EXP-2.7A_imasked as #4, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #6, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked as #3, grid size 128,128,128, pixel 2.7, shown
at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked as #8, grid size 128,128,128, pixel
2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked as #10, grid size 128,128,128,
pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked as #13, grid size
128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #15, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#17, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2.7A_imasked as #5, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
Opened Bb-EXP-2.7A_imasked as #9, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #7, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #11, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #18, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #19, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #20, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #21, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#22, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#23, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2.7A_imasked as #24, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Log from Tue Oct 4 11:33:43 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/jliu/Desktop/Export_appratus/Session/Fig3.cxs
Opened Bb-EXP-2.7A.mrc as #1, grid size 128,128,128, pixel 2.7, shown at step
1, values float32
Opened Bb-EXP-2.7A_imasked as #4, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #6, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked as #3, grid size 128,128,128, pixel 2.7, shown
at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked as #8, grid size 128,128,128, pixel
2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked as #10, grid size 128,128,128,
pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked as #13, grid size
128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #15, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#17, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2.7A_imasked as #5, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
Opened Bb-EXP-2.7A_imasked as #9, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #7, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #11, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #18, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #19, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #20, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #21, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#22, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#23, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2.7A_imasked as #24, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Log from Tue Oct 4 10:50:46 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/jliu/Desktop/Export_appratus/Session/Fig3.cxs
Opened Bb-EXP-2.7A.mrc as #1, grid size 128,128,128, pixel 2.7, shown at step
1, values float32
Opened Bb-EXP-2.7A_imasked as #4, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked as #6, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked as #3, grid size 128,128,128, pixel 2.7, shown
at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked as #8, grid size 128,128,128, pixel
2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked as #10, grid size 128,128,128,
pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked as #13, grid size
128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #15, grid
size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#17, grid size 128,128,128, pixel 2.7, shown at level 0.2, step 1, values
float32
Opened Bb-EXP-2.7A_imasked as #5, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #9, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #7, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Opened Bb-EXP-2.7A_imasked as #11, grid size 128,128,128, pixel 2.7, shown at
level 0.2, step 1, values float32
Log from Mon Oct 3 13:44:28 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jliu/Desktop/Export_appratus/Bb-EXP-2.7A.mrc
Opened Bb-EXP-2.7A.mrc as #1, grid size 128,128,128, pixel 2.7, shown at level
3.69, step 1, values float32
> view orient
> turn -x 90
> volume #1 level 0.2
> volume showOutlineBox true
> ui tool show "Segment Map"
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 60 of 200 regions.
Showing 60 of 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 60 surfaces
Grouped 9 regions
> ui tool show "Color Actions"
No visible atoms or bonds selected
[Repeated 43 time(s)]
> ui tool show "Color Actions"
> color sel orange
> color sel medium sea green
> color sel lime green
> color sel forest green
> color sel medium sea green
> color sel sea green
> select clear
Opened Bb-EXP-2.7A_imasked as #3, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> close #3
> show #!1 models
> show #!2 models
> close #2
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 60 of 200 regions.
Showing 60 of 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 60 surfaces
Grouped 8 regions
Grouped 2 regions
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> select clear
> close #2
> show #!1 models
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 200 of 200 regions.
Showing 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 200 surfaces
Grouped 9 regions
> hide #!1 models
> show #!1 models
> hide #!1 models
Opened Bb-EXP-2.7A_imasked as #3, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
> hide #!2 models
> hide #1.1 models
> color #3 forest green
> select #3
2 models selected
> ui tool show "Color Actions"
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> color sel medium sea green target s
> color sel sea green target s
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> show #1.1 models
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 200 of 200 regions.
Showing 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 200 surfaces
Drag select of 2491, 8295 of 25860 triangles, 2485, 1337 of 21840 triangles,
2527, 3336 of 12072 triangles, 2498, 2483 of 10648 triangles, 2500, 1675 of
10660 triangles, 2499, 5733 of 10644 triangles, 2536, 705 of 10488 triangles,
2360, 2109 of 7748 triangles, 2523, 70 of 7184 triangles, 2522, 1924 of 7184
triangles, 2228, 1683 of 4660 triangles, 2415, 2254 of 4020 triangles, 2186,
790 of 3004 triangles, 2379, 404 of 1236 triangles, 2393, 1032 of 1188
triangles, 2392, 1185 of 1192 triangles, 2396, 244 of 1124 triangles, 2082,
367 of 756 triangles, 2055, 647 of 808 triangles, 2068, 320 of 744 triangles,
2539, 180 of 424 triangles, 1 Bb-EXP-2.7A.mrc , 3 Bb-EXP-2.7A_imasked
> select clear
Grouped 9 regions
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,127,58,127
Opened Bb-EXP-2.7A_imasked as #4, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
> hide #!3 models
> hide #!2 models
> hide #1.1 models
> hide #!1 models
> ui mousemode right "crop volume"
> volume #4 region 0,0,0,127,127,127
> select #4
2 models selected
> color sel orange target s
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> hide #3.1 models
> hide #!4 models
> hide #4.1 models
> hide #1.1 models
> show #1.1 models
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 200 of 200 regions.
Showing 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 200 surfaces
> hide #!1 models
> show #!1 models
> close #4
> show #!3 models
> hide #1.1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #3.1 models
> ui mousemode right "crop volume"
> volume #3 region 0,0,0,127,126,127
> select #3
2 models selected
Please select one ore more regions
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> hide #!3 models
> show #!3 models
> close #3
> show #!1 models
> show #1.1 models
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,127,58,103
> volume #1 region 0,0,0,127,126,103
> volume #1 region 0,0,0,127,126,102
> volume #1 region 0,0,0,127,126,127
[Repeated 1 time(s)]
> volume #1 region 0,0,0,127,127,127
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 200 of 200 regions.
Showing 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 200 surfaces
Grouped 9 regions
Opened Bb-EXP-2.7A_imasked as #3, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!2 models
> show #!1 models
Opened Bb-EXP-2.7A_imasked as #4, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
> hide #1.1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select add #3
193 models selected
> select add #2
195 models selected
> select subtract #2
2 models selected
> close #2
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 200 of 200 regions.
Showing 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 200 surfaces
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> select add #3
2 models selected
> select clear
> select #3
2 models selected
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #4.1 models
> show #!4 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
Segmenting Bb-EXP-2.7A_imasked, density threshold 0.200000
Showing 180 region surfaces
1359 watershed regions, grouped to 180 regions
Showing Bb-EXP-2.seg - 180 regions, 180 surfaces
Drag select of 1968, 740 of 18936 triangles, 1970, 441 of 12684 triangles,
1978, 629 of 15272 triangles, 1989, 301 of 11880 triangles, 1977, 758 of 13160
triangles, 1988, 201 of 12268 triangles, 1981, 436 of 9340 triangles, 1975,
1700 of 11104 triangles, 1982, 5 of 8884 triangles, 1994, 1171 of 9748
triangles, 1996, 980 of 6776 triangles, 1743, 604 of 5516 triangles, 1881, 956
of 4276 triangles, 1869, 743 of 2908 triangles, 3 Bb-EXP-2.7A_imasked
> select clear
Grouped 6 regions
Opened Bb-EXP-2_imasked as #5, grid size 128,128,128, pixel 2.7, shown at step
1, values float32
Opened Bb-EXP-2_imasked as #6, grid size 128,128,128, pixel 2.7, shown at step
1, values float32
> hide #!5 models
> show #!5 models
> hide #!5 models
> close #2
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> close #6
> close #5
> show #!4 models
> hide #!4 models
> show #4.1 models
> show #!3 models
> hide #!4 models
> hide #4.1 models
Segmenting Bb-EXP-2.7A_imasked, density threshold 0.200000
Showing 180 region surfaces
1359 watershed regions, grouped to 180 regions
Showing Bb-EXP-2.seg - 180 regions, 180 surfaces
Grouped 9 regions
Opened Bb-EXP-2_imasked as #5, grid size 128,128,128, pixel 2.7, shown at step
1, values float32
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
Opened Bb-EXP-2_imasked as #6, grid size 128,128,128, pixel 2.7, shown at step
1, values float32
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> color sel orange target s
> select add #6
173 models selected
> color sel orange target s
> select clear
> show #!5 models
> show #4.1 models
> hide #4.1 models
> hide #!4 models
> show #!4 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #4.1 models
> hide #!5 models
> hide #!6 models
> hide #!3 models
> show #!6 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #4.1 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #4.1 models
> hide #!5 models
> hide #!6 models
> show #!3 models
> close #3
> show #!4 models
> show #4.1 models
> show #!5 models
> show #!6 models
> show #!2 models
> hide #!2 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #!5 models
> show #!5 models
> show #4.1 models
> hide #4.1 models
> hide #!6 models
> hide #!5 models
> show #4.1 models
> show #!5 models
> hide #4.1 models
> hide #!4 models
Segmenting Bb-EXP-2_imasked, density threshold 0.200000
Showing 171 region surfaces
1225 watershed regions, grouped to 171 regions
Showing Bb-EXP-2_imasked.seg - 171 regions, 171 surfaces
> surface dust #5 size 27
[Repeated 2 time(s)]Grouped 6 regions
Grouped 2 regions
[Repeated 1 time(s)]Opened Bb-EXP-2_imasked_imasked as #3, grid size
128,128,128, pixel 2.7, shown at step 1, values float32
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!6 models
> show #!5 models
> show #!3 models
> show #!2 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!5 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> close #3
> show #!2 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select clear
Opened Bb-EXP-2_imasked_imasked as #3, grid size 128,128,128, pixel 2.7, shown
at step 1, values float32
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #4.1 models
> hide #!4 models
> hide #!3 models
> select add #2
165 models selected
> select subtract #2
Nothing selected
> hide #!5 models
> show #!5 models
> show #4.1 models
> hide #!5 models
> color medium sea green target s
> color sea green target s
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> select add #6
2 models selected
> color sel orange target s
> hide #4.1 models
> show #!5 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #4.1 models
> hide #4.1 models
> select #5
2 models selected
> select clear
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> show #!3 models
> hide #!4 models
> hide #4.1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5
2 models selected
> select clear
> hide #!6 models
> hide #!3 models
> show #4.1 models
> hide #4.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #4.1 models
> hide #!3 models
> show #4.1 models
> hide #!4 models
> hide #4.1 models
> show #4.1 models
> hide #!5 models
> hide #!4 models
> hide #4.1 models
> show #!6 models
> hide #!6 models
> show #4.1 models
> hide #4.1 models
> show #!5 models
> show #!3 models
> hide #!5 models
> hide #!4 models
> close #3
> show #!2 models
> hide #!2 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> show #!4 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1.1 models
> hide #!1 models
> show #!2 models
Grouped 3 regions
Opened Bb-EXP-2_imasked_imasked as #3, grid size 128,128,128, pixel 2.7, shown
at step 1, values float32
> hide #!2 models
> select #3
2 models selected
> color sel orange target s
> select clear
> hide #!3 models
> show #!2 models
Drag select of 1816, 137 of 69652 triangles
Opened Bb-EXP-2_imasked_imasked as #7, grid size 128,128,128, pixel 2.7, shown
at step 1, values float32
> hide #!2 models
> surface dust #7 size 27
Segmenting Bb-EXP-2_imasked, density threshold 0.200000
Showing 171 region surfaces
1225 watershed regions, grouped to 171 regions
Showing Bb-EXP-2_imasked.seg - 171 regions, 171 surfaces
> close #2
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #1.1 models
> hide #1.1 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!7 models
Segmenting Bb-EXP-2_imasked_imasked, density threshold 0.200000
Showing 164 region surfaces
1068 watershed regions, grouped to 164 regions
Showing Bb-EXP-2_imasked_imasked.seg - 164 regions, 164 surfaces
Segmenting Bb-EXP-2_imasked_imasked, density threshold 0.200000
Only showing 100 of 164 regions.
Showing 100 of 164 region surfaces
1068 watershed regions, grouped to 164 regions
Showing Bb-EXP-2_imasked_imasked.seg - 164 regions, 100 surfaces
Grouped 8 regions
Opened Bb-EXP-2_imasked_imasked_imasked as #8, grid size 128,128,128, pixel
2.7, shown at step 1, values float32
> hide #!7 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> hide #!1 models
> close #8
> show #!2 models
> show #!1 models
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> close #2
> show #!7 models
Segmenting Bb-EXP-2_imasked_imasked, density threshold 0.200000
Showing 164 region surfaces
1068 watershed regions, grouped to 164 regions
Showing Bb-EXP-2_imasked_imasked.seg - 164 regions, 164 surfaces
> hide #!2 models
> show #!2 models
> hide #!7 models
> show #!7 models
Grouped 8 regions
Opened Bb-EXP-2_imasked_imasked_imasked as #8, grid size 128,128,128, pixel
2.7, shown at step 1, values float32
> hide #!7 models
> hide #!2 models
> show #!2 models
> show #!7 models
Opened Bb-EXP-2_imasked_imasked_imasked as #9, grid size 128,128,128, pixel
2.7, shown at step 1, values float32
> hide #!7 models
> hide #!8 models
> hide #!2 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
Segmenting Bb-EXP-2_imasked_imasked, density threshold 0.200000
Showing 164 region surfaces
1068 watershed regions, grouped to 164 regions
Showing Bb-EXP-2_imasked_imasked.seg - 164 regions, 164 surfaces
> hide #!2 models
Segmenting Bb-EXP-2_imasked_imasked_imasked, density threshold 0.200000
Showing 156 region surfaces
951 watershed regions, grouped to 156 regions
Showing Bb-EXP-2_imasked_imasked_imasked.seg - 156 regions, 156 surfaces
Grouped 8 regions
Grouped 2 regions
Opened Bb-EXP-2_imasked_imasked_imasked_imasked as #10, grid size 128,128,128,
pixel 2.7, shown at step 1, values float32
> hide #!9 models
> hide #!2 models
> show #!2 models
> show #!9 models
> hide #!10 models
> select clear
> hide #!9 models
> show #!9 models
Opened Bb-EXP-2_imasked_imasked_imasked_imasked as #11, grid size 128,128,128,
pixel 2.7, shown at step 1, values float32
> hide #!9 models
> hide #!11 models
> show #!11 models
> hide #!2 models
> show #!10 models
> hide #!11 models
> hide #!10 models
> show #!11 models
Segmenting Bb-EXP-2_imasked_imasked_imasked_imasked, density threshold
0.200000
Showing 147 region surfaces
895 watershed regions, grouped to 147 regions
Showing Bb-EXP-2_imasked_imasked_imasked_imasked.seg - 147 regions, 147
surfaces
Grouped 37 regions
Grouped 5 regions
Grouped 2 regions
Grouped 1 regions
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked as #12, grid size
128,128,128, pixel 2.7, shown at step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked as #13, grid size
128,128,128, pixel 2.7, shown at step 1, values float32
> hide #!11 models
> hide #!12 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!13 models
> show #!13 models
> show #!2 models
> hide #!13 models
> show #!13 models
> hide #!2 models
> show #!12 models
> hide #!13 models
> select #12
2 models selected
> select clear
Drag select of 12 Bb-EXP-2_imasked_imasked_imasked_imasked_imasked
> select clear
> select #12
2 models selected
Segmenting Bb-EXP-2_imasked_imasked_imasked_imasked_imasked, density threshold
0.200000
Showing 41 region surfaces
97 watershed regions, grouped to 41 regions
Showing Bb-EXP-2_imasked_imasked_imasked_imasked_imasked.seg - 41 regions, 41
surfaces
> select clear
> hide #!12 models
> show #!13 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!13 models
> show #!12 models
Segmenting Bb-EXP-2_imasked_imasked_imasked_imasked_imasked, density threshold
0.200000
Showing 106 region surfaces
798 watershed regions, grouped to 106 regions
Showing Bb-EXP-2_imasked_imasked_imasked_imasked_imasked.seg - 106 regions,
106 surfaces
Grouped 19 regions
Grouped 2 regions
Grouped 15 regions
Grouped 5 regions
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #14, grid
size 128,128,128, pixel 2.7, shown at step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked as #15, grid
size 128,128,128, pixel 2.7, shown at step 1, values float32
> select clear
> hide #!12 models
> hide #!14 models
> hide #!2 models
> show #!14 models
> hide #!15 models
> select #14
2 models selected
> hide #!14 models
> show #!14 models
Segmenting Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.200000
Showing 69 region surfaces
555 watershed regions, grouped to 69 regions
Showing Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked.seg - 69
regions, 69 surfaces
Grouped 22 regions
Grouped 3 regions
Grouped 2 regions
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#16, grid size 128,128,128, pixel 2.7, shown at step 1, values float32
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#17, grid size 128,128,128, pixel 2.7, shown at step 1, values float32
> hide #!14 models
> hide #!16 models
> hide #!2 models
> show #!16 models
> hide #!17 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!14 models
> show #!13 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> show #!17 models
> show #!4 models
> show #4.1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> select #16
2 models selected
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #4.1 models
> hide #!16 models
> show #!16 models
> hide #!17 models
Segmenting Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.200000
Showing 69 region surfaces
555 watershed regions, grouped to 69 regions
Showing Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked.seg - 69
regions, 69 surfaces
> select clear
[Repeated 1 time(s)]Drag select of 729, 727, 723, 746, 602, 616, 626, 601,
615, 814, 808, 813, 16 Bb-
EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked
Opened Bb-EXP-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#18, grid size 128,128,128, pixel 2.7, shown at step 1, values float32
> hide #!16 models
> show #!16 models
> hide #!18 models
> show #!18 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!17 models
> hide #!18 models
> hide #!2 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!16 models
> select clear
> hide #!17 models
> hide #!18 models
> hide #!16 models
> show #!16 models
> close #16
> show #!15 models
> show #!14 models
> hide #!15 models
> hide #!14 models
> show #!14 models
> close #14
> show #!12 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> close #12
> show #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!9 models
> show #!11 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!11 models
> show #!18 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> hide #!18 models
> show #!17 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!4 models
> show #4.1 models
> hide #!4 models
> hide #4.1 models
> hide #!17 models
> show #!11 models
> hide #!11 models
> show #!10 models
> select #10
2 models selected
> turn -x 90
> color sel black target s
> select clear
> set bgColor white
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!10 models
> select add #8
2 models selected
> color sel dark gray target s
> show #!10 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> close #5
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> close #18
> show #!17 models
> hide #!17 models
> show #!17 models
> show #!15 models
> hide #!15 models
> show #!15 models
> select add #8
2 models selected
> select subtract #8
Nothing selected
> select add #15
2 models selected
> color sel spring green target s
> color sel lime green target s
> color sel medium sea green target s
> select clear
> show #!13 models
> select subtract #15
Nothing selected
> select add #13
2 models selected
> color sel medium sea green target s
> select #15
2 models selected
> select clear
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> close #9
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> close #11
> show #!7 models
> hide #!7 models
> close #7
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> close #2
> show #!1 models
> hide #!1 models
> view orient
> turn -x 90
[Repeated 1 time(s)]
> ui mousemode right "crop volume"
> volume #4 region 0,0,0,127,127,127
> turn -x 90
> volume #4 region 0,0,0,127,127,119
> view orient
> turn -x 90
> volume #4 region 0,0,1,127,127,119
> volume #4 region 62,0,1,127,127,119
> turn -x 90
[Repeated 3 time(s)]
> turn -y 90
[Repeated 2 time(s)]
> volume #4 region 62,0,1,127,127,127
> select #10
2 models selected
No segmentation chosen
[Repeated 1 time(s)]
> select clear
No segmentation chosen
[Repeated 1 time(s)]
> turn -y 90
> select #8
2 models selected
> select clear
> select #8
2 models selected
No segmentation chosen
> select clear
> select #8
2 models selected
> hide #!8 models
> hide #!10 models
> turn -y 90
[Repeated 2 time(s)]
> volume #4 region 41,0,1,127,127,127
> show #!8 models
> hide #!8 models
> show #1.1 models
> hide #1.1 models
> select add #1
4 models selected
> color sel light gray target s
[Repeated 1 time(s)]
> color #1 #d6d6d6 models transparency 0
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #4.1 models
> hide #!6 models
> hide #!13 models
> hide #!15 models
> hide #!17 models
> show #!3 models
> show #!4 models
> show #4.1 models
> show #!6 models
> show #!13 models
> show #!15 models
> show #!17 models
> hide #!3 models
> hide #!4 models
> hide #4.1 models
> hide #!6 models
> hide #!13 models
> hide #!15 models
> hide #!17 models
> show #1.1 models
> select clear
> volume #1 region 0,0,0,127,127,127
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,127,127,127
> volume #1 region 66,0,0,127,127,127
> volume #1 region 0,0,0,127,127,127
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 200 of 200 regions.
Showing 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 200 surfaces
Drag select of 2544, 2577 of 9884 triangles, 2360, 1974 of 6728 triangles,
2221, 1814 of 6580 triangles, 2357, 2162 of 6396 triangles, 2224, 1577 of 6492
triangles, 2354, 1410 of 6064 triangles, 2215, 1772 of 6124 triangles, 2219,
1853 of 5820 triangles, 1 Bb-EXP-2.7A.mrc
> hide #!1 models
> select clear
[Repeated 1 time(s)]
> view orient
[Repeated 2 time(s)]
> turn -y 90
[Repeated 4 time(s)]Drag select of 2550, 668 of 6936 triangles, 2469, 856 of
6348 triangles, 2423, 4743 of 5924 triangles, 2466, 2977 of 5972 triangles,
2551, 2662 of 5504 triangles, 2391, 3607 of 6588 triangles, 2283, 4948 of 5404
triangles, 2223, 4358 of 6916 triangles, 2460, 4099 of 5396 triangles, 2483,
1079 of 5028 triangles, 2220, 3787 of 6328 triangles, 2416, 35 of 5220
triangles, 2417, 1998 of 5144 triangles, 2415, 169 of 4932 triangles, 2185,
1799 of 4788 triangles, 2549, 2370 of 4876 triangles, 2400, 3401 of 5608
triangles, 2386, 3137 of 5584 triangles, 2381, 3519 of 5860 triangles, 2180,
541 of 4968 triangles, 2011, 2965 of 4180 triangles, 2021, 1162 of 4112
triangles, 2397, 2360 of 5192 triangles, 2398, 2464 of 4992 triangles, 1537,
1226 of 4276 triangles, 1525, 1760 of 4088 triangles, 1531, 1791 of 4112
triangles, 1532, 24 of 4112 triangles, 1535, 1234 of 4084 triangles, 2037, 17
of 3396 triangles, 2012, 1249 of 4016 triangles, 2026, 2378 of 3320 triangles,
1534, 319 of 4024 triangles, 2015, 2868 of 3232 triangles, 2032, 2868 of 3356
triangles, 1558, 1798 of 2880 triangles, 2033, 2266 of 2724 triangles, 2200,
369 of 2504 triangles, 1544, 79 of 1688 triangles, 1593, 936 of 1804
triangles, 1547, 319 of 1132 triangles
> view orient
[Repeated 1 time(s)]
> turn -y 90
[Repeated 4 time(s)]Drag select of 2536, 3500 of 6912 triangles, 2461, 4288 of
4952 triangles, 2341, 3812 of 4336 triangles, 1512, 2152 of 4100 triangles,
1604, 3026 of 3232 triangles, 2036, 2942 of 3472 triangles, 1536, 1921 of 3836
triangles, 2030, 2658 of 2932 triangles, 1539, 1649 of 2552 triangles, 2198,
1811 of 2384 triangles
Grouped 9 regions
> select clear
Grouped 15 regions
Grouped 4 regions
Grouped 2 regions
> select clear
Drag select of 2553, 222 of 27040 triangles, 2552, 277 of 21532 triangles,
2519, 240 of 9340 triangles, 2498, 218 of 9748 triangles, 2242, 347 of 4716
triangles, 2239, 128 of 4728 triangles, 2320, 145 of 4708 triangles, 2312, 123
of 4256 triangles, 2377, 227 of 3404 triangles, 1992, 41 of 2596 triangles,
2000, 190 of 2468 triangles, 1980, 34 of 2536 triangles, 1981, 59 of 2448
triangles, 1833, 248 of 2472 triangles, 2554, 424 of 57632 triangles, 3 Bb-
EXP-2_imasked_imasked
> select clear
[Repeated 2 time(s)]Drag select of 2534, 10611 of 10864 triangles, 2514, 9746
of 10748 triangles, 2524, 9361 of 10596 triangles, 2547, 10453 of 10648
triangles, 2545, 9578 of 10648 triangles, 2513, 10563 of 10660 triangles,
2523, 10135 of 10716 triangles, 2530, 10605 of 10644 triangles, 2499, 10060 of
10572 triangles, 2490, 708 of 12084 triangles, 2259, 185 of 5480 triangles,
2263, 188 of 5228 triangles, 2266, 79 of 5180 triangles, 2262, 361 of 4660
triangles, 2264, 56 of 4524 triangles, 2302, 2334, 2292, 2337, 2008, 2186,
2191, 2190, 2048, 2511, 193 of 424 triangles, 2515, 301 of 328 triangles,
2509, 56 of 280 triangles, 3 Bb-EXP-2_imasked_imasked
> select clear
Opened Bb-EXP-2.7A_imasked as #5, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
> hide #!3 models
> hide #!2 models
> hide #1.1 models
> hide #!5 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> volume #4 region 41,0,1,127,127,127
[Repeated 1 time(s)]
> volume #4 region 41,0,1,127,127,115
> set bgColor black
> ui mousemode right "crop volume"
> volume #4 region 0,0,1,127,127,115
> hide #4.1 models
> hide #!4 models
> show #!17 models
> volume #17 region 0,0,1,127,127,127
> show #!15 models
> hide #!15 models
> show #!15 models
> volume #17 region 0,0,1,127,127,127
> show #!13 models
> volume #15 region 0,2,1,127,127,127
> show #!10 models
> volume #13 region 0,0,1,127,127,127
> show #!8 models
> volume #10 region 0,0,1,127,127,127
> show #!6 models
> volume #8 region 0,0,1,127,127,127
> show #!1 models
> show #1.1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #4.1 models
> show #!5 models
> volume #1 region 0,0,0,127,127,127
[Repeated 1 time(s)]
> select clear
> hide #1.1 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!8 models
> hide #!6 models
> hide #!10 models
> hide #4.1 models
> show #4.1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #4.1 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> hide #!13 models
> hide #!15 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> close #5
> show #!1 models
> show #1.1 models
Segmenting Bb-EXP-2.7A.mrc, density threshold 0.200000
Only showing 200 of 200 regions.
Showing 200 region surfaces
1774 watershed regions, grouped to 200 regions
Showing Bb-EXP-2.7A.seg - 200 regions, 200 surfaces
> hide #!1 models
> select clear
Drag select of 2507, 4114 of 9884 triangles, 2386, 2556 of 6728 triangles,
2392, 3445 of 6580 triangles, 2384, 3013 of 6396 triangles, 2414, 3295 of 6492
triangles, 2382, 2991 of 6064 triangles, 2334, 833 of 6588 triangles, 2387,
2939 of 6124 triangles, 2391, 2429 of 5820 triangles, 2328, 993 of 6916
triangles, 2331, 595 of 6328 triangles, 2339, 376 of 5608 triangles, 2343, 307
of 5584 triangles, 2330, 463 of 5860 triangles, 2326, 359 of 5192 triangles
> select clear
[Repeated 6 time(s)]Drag select of 2530, 1001 of 11260 triangles, 2500, 1048
of 9880 triangles, 2514, 669 of 9340 triangles, 2524, 2088 of 8884 triangles,
2490, 1470 of 10052 triangles, 2538, 34 of 8108 triangles, 2493, 591 of 9748
triangles, 2497, 122 of 8204 triangles, 2537, 1272 of 8156 triangles, 2489,
1871 of 7348 triangles, 2544, 2238 of 7184 triangles, 2547, 456 of 7164
triangles, 2352, 41 of 5516 triangles, 2499, 82 of 4664 triangles, 2135, 956
of 2468 triangles, 2134, 308 of 2448 triangles, 2127, 952 of 2472 triangles
> select clear
Grouped 8 regions
Grouped 2 regions
Grouped 1 regions
Grouped 3 regions
> select clear
Opened Bb-EXP-2.7A_imasked as #5, grid size 128,128,128, pixel 2.7, shown at
step 1, values float32
> hide #!5 models
> show #!5 models
> hide #!2 models
> hide #1.1 models
> hide #!5 models
> show #!5 models
> color sel medium sea green target s
> select add #5
191 models selected
> color sel medium sea green target s
> select clear
[deleted to fit within ticket limits]
> open /Users/jliu/Desktop/Export_appratus/PDB/6s3l-q-exp.pdb
Summary of feedback from opening
/Users/jliu/Desktop/Export_appratus/PDB/6s3l-q-exp.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 111
MET A 133 1 23
Start residue of secondary structure not found: HELIX 2 2 SER A 140 ASN A 173
1 34
Start residue of secondary structure not found: HELIX 3 3 ARG A 179 LYS A 195
1 17
Start residue of secondary structure not found: HELIX 4 4 ARG A 198 GLY A 210
1 13
Start residue of secondary structure not found: HELIX 5 5 SER A 220 GLY A 262
1 43
45 messages similar to the above omitted
6s3l-q-exp.pdb title:
Structure of the core of the flagellar export apparatus from vibrio mimicus,
the flipqr-FLHB complex. [more info...]
Chain information for 6s3l-q-exp.pdb #28
---
Chain | Description
G H I J | flagellar biosynthetic protein fliq
> open /Users/jliu/Desktop/Export_appratus/PDB/6s3l-b-exp.pdb
Summary of feedback from opening
/Users/jliu/Desktop/Export_appratus/PDB/6s3l-b-exp.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 111
MET A 133 1 23
Start residue of secondary structure not found: HELIX 2 2 SER A 140 ASN A 173
1 34
Start residue of secondary structure not found: HELIX 3 3 ARG A 179 LYS A 195
1 17
Start residue of secondary structure not found: HELIX 4 4 ARG A 198 GLY A 210
1 13
Start residue of secondary structure not found: HELIX 5 5 SER A 220 GLY A 262
1 43
49 messages similar to the above omitted
6s3l-b-exp.pdb title:
Structure of the core of the flagellar export apparatus from vibrio mimicus,
the flipqr-FLHB complex. [more info...]
Chain information for 6s3l-b-exp.pdb #29
---
Chain | Description
K | flagellar biosynthetic protein FLHB
> hide #29 models
> show #29 models
> hide #14 models
> hide #!20 models
> show #!20 models
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> show #14 models
> hide #14 models
> show #14 models
> show #14,27-29#!12#!2.1-9,32-46 cartoons
> hide #14,27-29#!12#!2.1-9,32-46 atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2.45/C:297@OE1
1 atom, 1 residue, 1 model selected
> select #2.43/C:282@CE2
1 atom, 1 residue, 1 model selected
> select clear
> hide #!10 models
> show #!10 models
> select add #10
2 models selected
> transparency #10.1 0
> select clear
> select #19
2 models selected
> hide #!19 models
> show #!19 models
> transparency #19.1 100
> select clear
> select #15
2 models selected
> transparency #15.1 100
> select clear
> hide #!15 models
> show #!15 models
> show #16 models
> hide #16 models
> open /Users/jliu/Desktop/Export_appratus/PDB/RBM2_RBM3&collar_x46.pdb
Summary of feedback from opening
/Users/jliu/Desktop/Export_appratus/PDB/RBM2_RBM3&collar_x46.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA C 233
GLY C 258 1 26
Start residue of secondary structure not found: HELIX 2 2 THR C 405 GLY C 421
1 17
Start residue of secondary structure not found: SHEET 1 1 1 VAL C 262 ASP C
271 0
Start residue of secondary structure not found: SHEET 2 2 1 THR C 278 HIS C
281 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU C 293 GLU C
302 0
4 messages similar to the above omitted
Chain information for RBM2_RBM3&collar_x46.pdb
---
Chain | Description
30.1/C 30.2/C 30.3/C 30.4/C 30.5/C 30.6/C 30.7/C 30.8/C 30.9/C 30.10/C 30.11/C
30.12/C 30.13/C 30.14/C 30.15/C 30.16/C 30.17/C 30.18/C 30.19/C 30.20/C
30.21/C 30.22/C 30.23/C 30.24/C 30.25/C 30.26/C 30.27/C 30.28/C 30.29/C
30.30/C 30.31/C 30.32/C 30.33/C 30.34/C 30.35/C 30.36/C 30.37/C 30.38/C
30.39/C 30.40/C 30.41/C 30.42/C 30.43/C 30.44/C 30.45/C 30.46/C | No
description available
30.47/D | No description available
> close #2
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> show #!30 models
> hide #!30 models
> show #!30 models
> view orient
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> turn -x 90
> hide #!30.21 models
> show #!30.21 models
> hide #!30.21 models
> hide #!30.22 models
> hide #!30.23 models
> hide #!30.24 models
> hide #!30.25 models
> hide #!30.26 models
> hide #!30.27 models
> hide #!30.28 models
> hide #!30.29 models
> hide #!30.30 models
> hide #!30.31 models
> hide #!30.32 models
> hide #!30.33 models
> show #!30.33 models
> hide #!30.20 models
> hide #!30.19 models
> hide #!30.18 models
> hide #!30.17 models
> hide #!30.16 models
> hide #!30.15 models
> hide #!30.14 models
> hide #!30.13 models
> hide #!30.12 models
> hide #!30.11 models
> hide #!30.10 models
> hide #!30.41 models
> show #!30.41 models
> hide #30.47 models
> show #30.47 models
> hide #30.47 models
> show #30.47 models
> show #!30.32 models
> hide #!30.32 models
> show #!30.32 models
> hide #!30.32 models
> show #!30.32 models
> show #!30.10 models
> view orient
> turn -x 90
> hide #!30 models
> close #30
> open /Users/jliu/Desktop/Export_appratus/PDB/test.pdb
Summary of feedback from opening
/Users/jliu/Desktop/Export_appratus/PDB/test.pdb
---
warnings | End residue of secondary structure not found: HELIX 1 1 ALA C 233
GLY C 258 1 26
Start residue of secondary structure not found: HELIX 2 2 THR C 405 GLY C 421
1 17
Start residue of secondary structure not found: SHEET 1 1 1 VAL C 262 ASP C
271 0
Start residue of secondary structure not found: SHEET 2 2 1 THR C 278 HIS C
281 0
Start residue of secondary structure not found: SHEET 3 3 1 LEU C 293 GLU C
302 0
Start residue of secondary structure not found: SHEET 4 4 1 THR C 358 TYR C
366 0
6 messages similar to the above omitted
End residue of secondary structure not found: SHEET 4 4 1 THR C 358 TYR C 366
0
Start residue of secondary structure not found: HELIX 1 1 ALA C 233 GLY C 258
1 26
Start residue of secondary structure not found: HELIX 2 2 THR C 405 GLY C 421
1 17
Start residue of secondary structure not found: SHEET 1 1 1 VAL C 262 ASP C
271 0
Start residue of secondary structure not found: SHEET 6 6 1 ASP C 381 VAL C
391 0
Start residue of secondary structure not found: SHEET 7 7 1 THR C 429 ASN C
434 0
31 messages similar to the above omitted
Chain information for test.pdb
---
Chain | Description
2.1/C | No description available
2.2/C | No description available
2.3/C | No description available
2.4/C 2.5/C 2.6/C 2.7/C 2.8/C 2.9/C 2.10/C 2.11/C 2.12/C 2.13/C 2.14/C 2.15/C
2.16/C 2.17/C 2.18/C 2.19/C 2.20/C 2.21/C 2.22/C 2.23/C | No description
available
2.24/C | No description available
2.25/C | No description available
2.26/C | No description available
2.27/C | No description available
2.28/C | No description available
2.29/D | No description available
> hide #14 models
> hide #!12 models
> hide #27 models
> hide #28 models
> hide #29 models
> select add #2
36382 atoms, 36758 bonds, 64 pseudobonds, 4708 residues, 58 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98903,-0.017954,0.14664,-15.144,0.0010314,0.9934,0.11468,-12.139,-0.14773,-0.11327,0.98252,0.082526
> select clear
> select add #16
16118 atoms, 16339 bonds, 2297 residues, 1 model selected
> select subtract #16
Nothing selected
> select add #2
36382 atoms, 36758 bonds, 64 pseudobonds, 4708 residues, 58 models selected
> view matrix models
> #2,-0.9018,-0.40997,0.1367,3.8077,0.42879,-0.88823,0.16486,-69.433,0.053838,0.20729,0.9768,5.6668
> view matrix models
> #2,-0.86969,-0.48149,0.10863,4.5429,0.49122,-0.82274,0.286,-80.628,-0.048337,0.30209,0.95205,11.513
> view matrix models
> #2,-0.80967,-0.56847,0.14587,-1.7603,0.58348,-0.80645,0.095874,-62.318,0.063138,0.16274,0.98465,3.8815
> view matrix models
> #2,-0.96106,-0.27583,-0.016944,33.891,0.27185,-0.95465,0.12144,-63.3,-0.049672,0.11211,0.99245,1.9135
> view matrix models
> #2,-0.94057,-0.33911,-0.018032,32.267,0.33252,-0.93048,0.15377,-65.645,-0.068923,0.13863,0.98794,3.2512
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.94057,-0.33911,-0.018032,13.185,0.33252,-0.93048,0.15377,-68.372,-0.068923,0.13863,0.98794,12.105
> select subtract #2
Nothing selected
> select add #2
36382 atoms, 36758 bonds, 64 pseudobonds, 4708 residues, 58 models selected
> view matrix models
> #2,-0.94057,-0.33911,-0.018032,5.6346,0.33252,-0.93048,0.15377,-28.64,-0.068923,0.13863,0.98794,-0.30644
> view matrix models
> #2,-0.94057,-0.33911,-0.018032,9.1825,0.33252,-0.93048,0.15377,-34.307,-0.068923,0.13863,0.98794,1.465
> view matrix models
> #2,-0.94057,-0.33911,-0.018032,9.0223,0.33252,-0.93048,0.15377,-21.355,-0.068923,0.13863,0.98794,-2.5796
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.94006,-0.34099,-0.0032592,7.5404,0.33775,-0.93236,0.12896,-19.04,-0.047014,0.12013,0.99164,-3.7356
> view matrix models
> #2,-0.94128,-0.32829,-0.078854,15.332,0.31558,-0.93849,0.14013,-19.997,-0.12001,0.10701,0.98699,-2.6529
> select subtract #2
Nothing selected
> select add #2
36382 atoms, 36758 bonds, 64 pseudobonds, 4708 residues, 58 models selected
> view matrix models
> #2,-0.81231,-0.57735,-0.082616,8.0291,0.55225,-0.80696,0.20938,-27.061,-0.18755,0.12445,0.97434,-0.16708
> view matrix models
> #2,-0.76681,-0.63164,-0.11421,9.5737,0.6278,-0.77508,0.071549,-13.512,-0.13371,-0.016835,0.99088,-5.3809
> view matrix models
> #2,-0.76278,-0.64336,-0.065233,4.4364,0.57225,-0.71854,0.39526,-43.971,-0.30117,0.26416,0.91625,9.5021
> view matrix models
> #2,-0.79475,-0.59746,-0.10688,9.6925,0.60168,-0.79868,-0.0093974,-5.5326,-0.079745,-0.071774,0.99423,-7.2964
> view matrix models
> #2,-0.78596,-0.61061,-0.097084,8.3258,0.60707,-0.7919,0.066043,-13.138,-0.11721,-0.0070293,0.99308,-5.4276
> view matrix models
> #2,-0.82914,-0.55018,0.099184,-16.153,0.55897,-0.81303,0.16287,-17.44,-0.0089674,0.19048,0.98165,-3.6917
> select subtract #2
Nothing selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 29 atomic models, 15 maps.
[Repeated 1 time(s)]
> select add #2
36382 atoms, 36758 bonds, 64 pseudobonds, 4708 residues, 58 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 29 atomic models, 15 maps.
[Repeated 3 time(s)]
> ui tool show "Fit in Map"
> fitmap sel inMap #1
Fit molecules test.pdb (#2.1), test.pdb (#2.2), test.pdb (#2.3), test.pdb
(#2.4), test.pdb (#2.5), test.pdb (#2.6), test.pdb (#2.7), test.pdb (#2.8),
test.pdb (#2.9), test.pdb (#2.10), test.pdb (#2.11), test.pdb (#2.12),
test.pdb (#2.13), test.pdb (#2.14), test.pdb (#2.15), test.pdb (#2.16),
test.pdb (#2.17), test.pdb (#2.18), test.pdb (#2.19), test.pdb (#2.20),
test.pdb (#2.21), test.pdb (#2.22), test.pdb (#2.23), test.pdb (#2.24),
test.pdb (#2.25), test.pdb (#2.26), test.pdb (#2.27), test.pdb (#2.28),
test.pdb (#2.29) to map Bb-EXP-2.7A.mrc (#1) using 36382 atoms
average map value = 0.96, steps = 320
shifted from previous position = 19.1
rotated from previous position = 11.7 degrees
atoms outside contour = 9103, contour level = 0.2
Position of test.pdb (#2.1) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.2) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.3) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.4) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.5) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.6) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.7) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.8) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.9) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.10) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.11) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.12) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.13) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.14) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.15) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.16) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.17) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.18) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.19) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.20) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.21) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.22) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.23) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.24) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.25) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.26) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.27) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.28) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
Position of test.pdb (#2.29) relative to Bb-EXP-2.7A.mrc (#1) coordinates:
Matrix rotation and translation
0.99949763 0.02830331 -0.01426229 1.40976739
-0.02487396 0.97939233 0.20042939 -29.16740053
0.01964119 -0.19997395 0.97960433 8.74479032
Axis -0.98782218 -0.08364218 -0.13119193
Axis point 0.00000000 28.51828746 148.49856989
Rotation angle (degrees) 11.69312208
Shift along axis -0.10022056
> select clear
> select add #2
36382 atoms, 36758 bonds, 64 pseudobonds, 4708 residues, 58 models selected
> surface (#2.28#!2.1-27,29 & sel)
> select clear
> view orient
> turn -x 90
> select clear
> show #27 models
> show #28 models
> show #29 models
> show #!12 models
> show #14 models
> show #16 models
> hide #16 models
> close #16
> select clear
> select #26
2 models selected
> select #26
2 models selected
> select clear
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> select add #18
2 models selected
> select subtract #18
Nothing selected
> select add #19
2 models selected
> select subtract #19
Nothing selected
> select add #19
2 models selected
> select subtract #19
Nothing selected
> select add #20
2 models selected
> select subtract #20
Nothing selected
> select add #20
2 models selected
> select subtract #20
Nothing selected
> select add #21
2 models selected
> transparency #21.1 0
> select clear
[Repeated 1 time(s)]
> show #!13 models
> select clear
> select #13
2 models selected
> hide #!15 models
> select subtract #13
Nothing selected
> show #!15 models
> hide #!19 models
> show #!19 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> select add #19
2 models selected
> transparency #19.1 0
> select subtract #19
Nothing selected
> select add #19
2 models selected
> transparency #19.1 0
> select clear
> select add #19
2 models selected
> select subtract #19
Nothing selected
> select add #19
2 models selected
> transparency #19.1 0
> select clear
> select #19
2 models selected
> select subtract #19
Nothing selected
> select add #19
2 models selected
> transparency #19.1 100
> select add #20
4 models selected
> select subtract #19
2 models selected
> select subtract #20
Nothing selected
> select add #18
2 models selected
> transparency #18.1 0
> select clear
> select #18
2 models selected
> ui tool show "Color Actions"
> color sel medium sea green
> select clear
> select add #27
1948 atoms, 1993 bonds, 251 residues, 1 model selected
> color sel hot pink
> select clear
> select add #28
2896 atoms, 2968 bonds, 356 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> select clear
> select #2.18/C:376@CD
1 atom, 1 residue, 1 model selected
> select add #6
1 atom, 1 residue, 4 models selected
> select add #7
1 atom, 1 residue, 6 models selected
> select add #11
1 atom, 1 residue, 8 models selected
> select add #10
1 atom, 1 residue, 10 models selected
> select subtract #10
1 atom, 1 residue, 8 models selected
> select add #24
1 atom, 1 residue, 10 models selected
> transparency (#!2.18 & sel) 90
> select clear
[Repeated 1 time(s)]
> select add #6
2 models selected
> select add #7
4 models selected
> select add #11
6 models selected
> select add #9
8 models selected
> select add #24
10 models selected
> transparency #6.1#7.1#9.1#11.1#24.1 100
> transparency #6.1#7.1#9.1#11.1#24.1 90
> select clear
[Repeated 1 time(s)]
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1b' for virtual key 53 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x9' for virtual key 48 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select clear
> hide #!12 models
> close #12
> open /Users/jliu/Desktop/Export_appratus/PDB/flhA_cytosolic.pdb
> /Users/jliu/Desktop/Export_appratus/PDB/flhA_linker.pdb
> /Users/jliu/Desktop/Export_appratus/PDB/flhA_mem.pdb
Summary of feedback from opening
/Users/jliu/Desktop/Export_appratus/PDB/flhA_cytosolic.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 4
LYS A 6 1 3
Start residue of secondary structure not found: HELIX 2 2 ILE A 9 TYR A 12 1 4
Start residue of secondary structure not found: HELIX 3 3 LYS A 18 PHE A 34 1
17
Start residue of secondary structure not found: HELIX 4 4 ALA A 40 TYR A 63 1
24
Start residue of secondary structure not found: HELIX 5 5 SER A 67 PHE A 70 1
4
103 messages similar to the above omitted
Summary of feedback from opening
/Users/jliu/Desktop/Export_appratus/PDB/flhA_linker.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 4
LYS A 6 1 3
Start residue of secondary structure not found: HELIX 2 2 ILE A 9 TYR A 12 1 4
Start residue of secondary structure not found: HELIX 3 3 LYS A 18 PHE A 34 1
17
Start residue of secondary structure not found: HELIX 4 4 ALA A 40 TYR A 63 1
24
Start residue of secondary structure not found: HELIX 5 5 SER A 67 PHE A 70 1
4
337 messages similar to the above omitted
Summary of feedback from opening
/Users/jliu/Desktop/Export_appratus/PDB/flhA_mem.pdb
---
warnings | Start residue of secondary structure not found: HELIX 11 11 LEU A
289 PHE A 304 1 16
Start residue of secondary structure not found: HELIX 12 12 THR A 310 SER A
351 1 42
Start residue of secondary structure not found: HELIX 13 13 VAL A 373 ILE A
375 1 3
Start residue of secondary structure not found: HELIX 14 14 GLU A 383 PHE A
399 1 17
Start residue of secondary structure not found: HELIX 15 15 ASP A 468 LYS A
476 1 9
265 messages similar to the above omitted
Chain information for flhA_cytosolic.pdb #12
---
Chain | Description
A B C D E F G H I | No description available
Chain information for flhA_linker.pdb #16
---
Chain | Description
A B C D E F G H I | No description available
Chain information for flhA_mem.pdb #30
---
Chain | Description
A B C D E F G H I | No description available
> select add #30
40293 atoms, 40554 bonds, 2592 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select subtract #30
Nothing selected
> select add #16
10944 atoms, 11079 bonds, 675 residues, 1 model selected
> color sel hot pink
> select clear
> select add #12
48618 atoms, 48978 bonds, 3006 residues, 1 model selected
> ui tool show "Color Actions"
> color sel steel blue
> select clear
> select add #12
48618 atoms, 48978 bonds, 3006 residues, 1 model selected
> select add #30
88911 atoms, 89532 bonds, 5598 residues, 2 models selected
> select add #16
99855 atoms, 100611 bonds, 6273 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select add #30
40293 atoms, 40554 bonds, 2592 residues, 1 model selected
> select subtract #30
Nothing selected
> select add #12
48618 atoms, 48978 bonds, 3006 residues, 1 model selected
> ui tool show "Color Actions"
> color sel olive
> select clear
[Repeated 2 time(s)]
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 97 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select clear
> show #!13 models
> hide #!13 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
[Repeated 1 time(s)]
> select add #29
1492 atoms, 1520 bonds, 193 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> select clear
[Repeated 1 time(s)]
> save /Users/jliu/Desktop/Export_appratus/Session/3B.cxs includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot
data[attr] = getattr(self, attr).value
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 190, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '···········1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8ec4c5d4f0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x7f8eb62842e0> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
Populating font family aliases took 381 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot
data[attr] = getattr(self, attr).value
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 190, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '···········1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8ec4c5d4f0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x7f8eb62842e0> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /Users/jliu/Desktop/Export_appratus/Session/3B.cxs includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot
data[attr] = getattr(self, attr).value
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 190, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '···········1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8ec4c5d4f0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x7f8eb62842e0> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot
data[attr] = getattr(self, attr).value
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 190, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '···········1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8ec4c5d4f0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x7f8eb62842e0> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /Users/jliu/Desktop/Export_appratus/Session/3B.cxs includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot
data[attr] = getattr(self, attr).value
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 190, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '···········1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8ec4c5d4f0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x7f8eb62842e0> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot
data[attr] = getattr(self, attr).value
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 190, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '···········1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8ec4c5d4f0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x7f8eb62842e0> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /Users/jliu/Desktop/Export_appratus/Session/3B.cxs includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot
data[attr] = getattr(self, attr).value
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 190, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '···········1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8ec4c5d4f0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x7f8eb62842e0> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 3391, in take_snapshot
data[attr] = getattr(self, attr).value
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 190, in _get_value
return self.string_to_value(self._line_edit.text())
ValueError: invalid literal for int() with base 10: '···········1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f8ec4c5d4f0> -> <chimerax.segger.segment_dialog.VolumeSegmentationDialog
object at 0x7f8eb62842e0> 'segment map': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x7f8ec4c5d4f0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x7f8eb62842e0> 'segment map'
ValueError: error processing: 'tools' -> -> 'segment map': Error while saving
session data for 'tools' -> -> 'segment map'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Window position QRect(1291,1583 100x30) outside any known screen, using
primary screen
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
System Firmware Version: 451.140.1.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 14 days 6:07
Graphics/Displays:
Radeon Pro 580:
Chipset Model: Radeon Pro 580
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1X-025
EFI Driver Version: 01.00.931
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-Clipper: 0.18.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
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-ISOLDE: 1.4
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Segger session save: invalid literal for int |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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The session failed to save because a non-integer values was typed into one of the Segger dialog fields and it gave an error while saving the session trying to convert that setting to an integer. This was fixed in June (after the ChimeraX 1.4 release) and the fix is in the ChimeraX daily builds.
Duplicate of #6982