Opened 2 years ago

Last modified 2 years ago

#9763 assigned defect

Volume: self.data is None

Reported by: chimerax-bug-report@… Owned by: Utz Ermel
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc as #1.1.1, grid size
512,512,150, pixel 12,12,12, shown at level 0.000214, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> volume #1.1.1 style surface

> volume #1.1.1 level 1.267

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc  

> volume #1.1.1 level 0.8983

> transparency sel 50

> volume sel style surface

> transparency sel 0

> select clear

> ui tool show "Map Eraser"

> volume erase #1.1.1 center 3008.3,3660.5,7.1888 radius 752.43

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy as #3, grid size
512,512,150, pixel 12,12,12, shown at step 1, values float32  

> volume erase #3 center 1660.7,2293.3,1951.2 radius 749.57

> volume erase #3 center 1498.7,1873.9,1649.4 radius 749.57

> surface dust #3 size 120

> volume #1.1.1 level 1.052

> volume #3 level 1.228

> volume #3 level 1.106

> surface dust #1.1.1 size 120

> surface dust #3 size 120

> ui tool show "Segment Map"

Segmenting PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy, density
threshold 1.105586  
Only showing 60 of 183 regions.  
Showing 60 of 183 region surfaces  
1183 watershed regions, grouped to 183 regions  
Showing PDC_12_ts_005_bin8_WBP_corrected_object_1 copy.seg - 183 regions, 60
surfaces  
Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1650,
2018 of 9076 triangles, 1481, 336 of 5780 triangles, 1680, 1633, 1565, 1028 of
7448 triangles, 1619, 2689 of 6864 triangles, 1665, 1685, 1594, 5789 of 6356
triangles, 1578, 1516 of 5704 triangles, 1485, 1659, 1655, 1661, 3888 of 5160
triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> select clear

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1578,
1673 of 5704 triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> select clear

Segmenting PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy, density
threshold 1.105586  
Only showing 60 of 148 regions.  
Showing 60 of 148 region surfaces  
1183 watershed regions, grouped to 148 regions  
Showing PDC_12_ts_005_bin8_WBP_corrected_object_1 copy.seg - 148 regions, 60
surfaces  
Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1603,
4038 of 7212 triangles, 1554, 1700, 3796 of 6608 triangles, 3
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  
Grouped 3 regions  
Segmenting PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy, density
threshold 1.105586  
Showing 42 region surfaces  
1183 watershed regions, grouped to 42 regions  
Showing PDC_12_ts_005_bin8_WBP_corrected_object_1 copy.seg - 42 regions, 42
surfaces  
Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1803,
5099 of 58120 triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  
Segmenting PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy, density
threshold 1.105586  
Only showing 60 of 62 regions.  
Showing 60 of 62 region surfaces  
1183 watershed regions, grouped to 62 regions  
Showing PDC_12_ts_005_bin8_WBP_corrected_object_1 copy.seg - 62 regions, 60
surfaces  

> surface dust #1.1.1 size 120

> surface dust #3 size 120

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1786,
1805 of 25216 triangles, 1753, 1784, 12114 of 21280 triangles, 1783, 9860 of
17864 triangles, 1785, 1572 of 23424 triangles, 1788, 1202 of 19248 triangles,
1726, 2698 of 13304 triangles, 1776, 1917 of 16484 triangles, 1705, 5765 of
9092 triangles, 1774, 9936 of 11684 triangles, 1731, 1760, 1690, 4446 of 5920
triangles, 1768, 1751, 6154 of 6296 triangles, 1735, 6616 of 6800 triangles,
1358, 1791, 2488 of 3240 triangles, 3
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> ui tool show "Color Actions"

> color sel bisque

> color sel pink

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1779,
14846 of 31000 triangles, 1785, 4251 of 23424 triangles, 1789, 743 of 17176
triangles, 1776, 1790, 9909 of 11656 triangles, 1768, 135 of 8692 triangles,
1735, 2668 of 6800 triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc
copy  

> color sel peach puff

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1779,
1732 of 31000 triangles, 1785, 21504 of 23424 triangles, 1789, 2034 of 17176
triangles, 1776, 1790, 4886 of 11656 triangles, 1768, 7586 of 8692 triangles,
1751, 6154 of 6296 triangles, 1735, 1531, 3623 of 4388 triangles, 1745, 2059
of 5308 triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel peach puff

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1789, 926
of 17176 triangles, 1676, 6939 of 9456 triangles, 3
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel peach puff

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1783,
10405 of 17864 triangles, 1782, 4340 of 12448 triangles, 1774, 3520 of 11684
triangles, 1769, 3444 of 6304 triangles, 3
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel pink

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1771,
11914 of 11964 triangles, 1761, 6642 of 10724 triangles, 1773, 1764, 9577 of
13080 triangles, 1727, 1628, 1777, 281 of 6148 triangles, 1767, 1671, 1438 of
3560 triangles, 1602, 1781, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc
copy  

> color sel peach puff

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1718, 3
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel peach puff

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1693,
12338 of 16156 triangles, 1698, 1586, 3451 of 7740 triangles, 1606, 3169 of
3756 triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel pink

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1762,
1966 of 2452 triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel peach puff

> select clear

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1780,
1369 of 36076 triangles, 1779, 22262 of 31000 triangles, 1753, 15174 of 15964
triangles, 1784, 4596 of 21280 triangles, 1785, 4844 of 23424 triangles, 1789,
8697 of 17176 triangles, 1776, 1705, 6561 of 9092 triangles, 1790, 1774, 696
of 11684 triangles, 1731, 5751 of 10216 triangles, 1760, 1690, 5483 of 5920
triangles, 1768, 1735, 1358, 2409 of 2580 triangles, 3
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> select clear

> select add #2.5

1 model selected  

> color sel peach puff

> color sel pink

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1751, 389
of 6296 triangles, 1762, 2248 of 2452 triangles, 3
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel pink

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1786, 440
of 25216 triangles, 1784, 6437 of 21280 triangles, 1726, 8039 of 13304
triangles, 1646, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel pink

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1789,
1447 of 17176 triangles, 1776, 301 of 16484 triangles, 1790, 10449 of 11656
triangles, 1735, 121 of 6800 triangles, 3
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel pink

> select clear

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1793,
2390 of 4832 triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel pink

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc , 1753,
10185 of 15964 triangles, 1783, 1782, 3464 of 12448 triangles, 1705, 1338 of
9092 triangles, 1774, 1769, 1794 of 6304 triangles, 1791, 1000 of 3240
triangles, 3 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> color sel pink

> select clear

> ui tool show "Map Eraser"

Can only have one displayed volume when erasing  

[Repeated 9 time(s)]

> undo

[Repeated 1 time(s)]

Can only have one displayed volume when erasing  

> close session

> open
> D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_bin8_WBP_corrected_seg__tomosegresult1.hdf

Opened 230213_PDC_12_ts_005_bin8_WBP_corrected_seg__tomosegresult1.hdf as #1,
grid size 512,512,150, pixel 12, shown at level 0.791, step 2, values float32  

> surface dust #1 size 120

> volume #1 level 0.7398

> surface dust #1 size 120

[Repeated 1 time(s)]

> volume #1 level 1.198

> close session

> open
> D:/xinglab/paper/data/segmentation/230213_12_005/PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc as #1, grid size
512,512,150, pixel 12,12,12, shown at level 0.00021, step 2, values float32  

> surface dust #1 size 120

> volume #1 level 1.054

Drag select of 1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc  

> select clear

> ui tool show "Segment Map"

Segmenting PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc, density threshold
1.054413  
Only showing 60 of 62 regions.  
Showing 60 of 62 region surfaces  
1206 watershed regions, grouped to 62 regions  
Showing PDC_12_ts_005_bin8_WBP_corrected_object_1.seg - 62 regions, 60
surfaces  

> surface dust #1 size 120

Smoothing and grouping, standard deviation 9 voxels  
Showing 49 region surfaces  
Got 49 regions after smoothing 9 voxels.  

> surface dust #1 size 120

[Repeated 8 time(s)]

> volume #1 level 0.8727

Drag select of 1811, 2875 of 22020 triangles, 1823, 1547 of 17632 triangles,
1786, 677 of 12252 triangles, 1796, 1756, 2277 of 6452 triangles, 1829, 11414
of 51472 triangles, 1827, 1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc  

> volume #1 level 1.643

Ungrouped to 17 regions  

QWindowsWindow::setGeometry: Unable to set geometry 602x266+3244+208 (frame:
618x305+3236+177) on QWidgetWindow/"QDockWidgetClassWindow" on "AOC TV".
Resulting geometry: 602x249+3244+208 (frame: 618x288+3236+177) margins: 8, 31,
8, 8 minimum size: 596x249 maximum size: 524287x249
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=288), mintrack=POINT(x=612, y=288)))  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> artiax add tomo #1

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc as #3.1.1, grid size
512,512,150, pixel 12,12,12, shown at level 0.000214, step 1, values float32  

> artiax tomo #3.1.1 sliceDirection 0,0,1

> artiax view xy

> select clear

> volume #3.1.1 style surface

> volume #3.1.1 level 0.9545

Drag select of 1808, 1800, 1806, 1825, 1819, 1809, 1803, 1814, 1695, 1812,
1782, 1793, 1701, 1794, 1816, 1802, 1805, 1824, 6008 of 13368 triangles, 1700,
1777, 1762, 1798, 1688, 1669, 1820, 1511, 1785, 1315, 1817, 1746, 1815, 1750,
1795, 1620, 1818, 1831, 1828, 1830, 1832, 1826, 1697, 1807, 1770, 1758, 1781,
1566, 1552, 854, 1791, 1761, 1648, 1731, 1747, 1788, 1766, 1810, 1412, 1754,
1774, 3.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc  
Drag select of 1808, 1800, 1806, 1825, 1819, 1809, 1803, 1814, 1695, 1812,
1782, 1793, 1701, 1794, 1816, 1802, 1805, 1824, 1700, 1777, 1762, 1798, 1688,
1669, 1820, 1511, 1785, 1315, 1817, 1746, 1815, 1750, 1795, 1620, 1818, 1831,
1828, 1830, 1832, 1826, 1697, 1807, 1770, 1758, 1781, 1566, 1552, 854, 1791,
1761, 1648, 1731, 1747, 1788, 1766, 1810, 1412, 1754, 1774, 3.1.1
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc  
[Repeated 1 time(s)]

> surface dust #3.1.1 size 120

> ui tool show "Hide Dust"

> surface dust #3.1.1 size 12

> surface dust #3.1.1 size 46.89

[Repeated 4 time(s)]

> select clear

> surface dust #3.1.1 size 46.89

[Repeated 17 time(s)]

> ui tool show "Map Eraser"

> volume erase #3.1.1 center 3495.6,1733.3,879.84 radius 265.94

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy as #4, grid size
512,512,150, pixel 12,12,12, shown at step 1, values float32  

> volume erase #4 center 3447.9,1686.4,874.99 radius 264.19

[Repeated 2 time(s)]

> volume erase #4 center 3474.3,1758.7,889.78 radius 264.19

[Repeated 9 time(s)]

> volume #4 level 1.435

> volume erase #4 center 4700.4,1155.3,429.65 radius 337.92

[Repeated 2 time(s)]

> volume erase #4 center 2353.9,3337.6,892.02 radius 337.92

[Repeated 1 time(s)]

> close session

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc as #1.1.1, grid size
512,512,150, pixel 12,12,12, shown at level 0.000214, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> volume #1.1.1 style surface

> volume #1.1.1 level 0.9249

> surface dust #1.1.1 size 120

Drag select of 1.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc  

> volume #1.1.1 level 1.147

> volume #1.1.1 level 0.6216

> ui tool show "Color Actions"

[Repeated 1 time(s)]

> vop gaussian #1.1.1 sdev 36

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc gaussian as #2, grid size
512,512,150, pixel 12,12,12, shown at step 1, values float32  

> volume #2 level 0.6163

> volume #2 step 8

> volume #2 level 0.111

> volume #2 step 1

> volume #2 level 0.111

> volume #2 level 0.187

> volume #!2 style surface

> volume #!2 style image

> volume #!2 style mesh

> volume #!2 style surface

> ui tool show "Side View"

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting shadows true

> graphics silhouettes false

Drag select of 2 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc gaussian  

> close #2

> volume #1.1.1 level 0.8065

> volume #1.1.1 level 0.7917

> ui tool show "Segment Map"

No segmentation chosen  
[Repeated 1 time(s)]Segmenting PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc,
density threshold 0.791725  
Only showing 60 of 62 regions.  
Showing 60 of 62 region surfaces  
1219 watershed regions, grouped to 62 regions  
Showing PDC_12_ts_005_bin8_WBP_corrected_object_1.seg - 62 regions, 60
surfaces  

> surface dust #1.1.1 size 120

[Repeated 5 time(s)]Smoothing and grouping, standard deviation 9 voxels  
Showing 49 region surfaces  
Got 49 regions after smoothing 9 voxels.  

> surface dust #1.1.1 size 120

[Repeated 7 time(s)]

> ui tool show "Map Eraser"

> volume erase #1.1.1 center 2949.5,5610.7,512.63 radius 759.96

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy as #4, grid size
512,512,150, pixel 12,12,12, shown at step 1, values float32  

> volume erase #4 center 2949.5,5610.7,512.63 radius 758.78

[Repeated 2 time(s)]

> volume erase #4 center 2606,4090,1234 radius 599.04

QWindowsWindow::setGeometry: Unable to set geometry 602x266+3239+202 (frame:
618x305+3231+171) on QWidgetWindow/"QDockWidgetClassWindow" on "AOC TV".
Resulting geometry: 602x249+3239+202 (frame: 618x288+3231+171) margins: 8, 31,
8, 8 minimum size: 596x249 maximum size: 524287x249
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=288), mintrack=POINT(x=612, y=288)))  

> volume erase #4 center 2596.2,4061.8,1230.1 radius 599.04

[Repeated 2 time(s)]Drag select of 1834, 10552 of 23184 triangles, 1822, 1842,
4425 of 18832 triangles, 1819, 7259 of 13112 triangles, 1805, 7088 of 12840
triangles, 1785, 995 of 9324 triangles, 1816, 1777, 4649 of 10284 triangles,
1793, 2274 of 6912 triangles, 1636, 150 of 5928 triangles, 1843, 1838, 2852 of
4016 triangles, 1844, 13879 of 54116 triangles, 1848, 5697 of 38312 triangles,
1849, 2725 of 36808 triangles, 1845, 1847, 17218 of 17232 triangles, 4
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> select clear

Drag select of 1822, 6837 of 17316 triangles, 1842, 14272 of 18832 triangles,
1819, 9708 of 13112 triangles, 1827, 216 of 13216 triangles, 1816, 1793, 4702
of 6912 triangles, 1848, 9136 of 38312 triangles, 1849, 17928 of 36808
triangles, 1847, 15550 of 17232 triangles, 4
PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> volume #4 level 0.8805

> volume #1.1.1 level 0.9915

> select clear

> ui tool show "Segment Map"

Saving 49 regions to mrc file...  
Opened PDC_12_ts_005_bin8_WBP_corrected_object_1_49_regions.mrc as #3, grid
size 471,418,97, pixel 12,12,12, shown at step 1, values float32  
Wrote PDC_12_ts_005_bin8_WBP_corrected_object_1_49_regions.mrc  

> volume #3 level 1.282

> volume #3 level 1.23

> close #4

> close #1.1.1

> surface dust #3 size 120

[Repeated 5 time(s)]

> volume #3 level 1.164

> open
> D:/xinglab/paper/data/segmentation/230213_12_005/PDC_12_ts_005_bin8_WBP_corrected_object_1_49_regions.mrc

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1_49_regions.mrc as #4, grid
size 471,418,97, pixel 12,12,12, shown at level 1.06, step 2, values float32  

> close #3

> close #4

> close session

> open
> D:/xinglab/paper/data/segmentation/230213_12_005/PDC_12_ts_005_bin8_WBP_corrected_object_1_49_regions.mrc

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1_49_regions.mrc as #1, grid
size 471,418,97, pixel 12,12,12, shown at level 1.06, step 2, values float32  

> surface dust #1 size 120

Drag select of 1 PDC_12_ts_005_bin8_WBP_corrected_object_1_49_regions.mrc  

> close session

> open
> D:\xinglab\paper\data\segmentation\230213_12_005\PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc
> format mrc

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc as #1, grid size
512,512,150, pixel 12,12,12, shown at level 0.00021, step 2, values float32  

> volume #1 level 0.8727

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> ui tool show "Map Eraser"

> volume erase #1 center 2544,4119,803.08 radius 510.57

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy as #4, grid size
512,512,150, pixel 12,12,12, shown at step 1, values float32  

> volume erase #4 center 3035.8,5208.6,1064.5 radius 509.95

> volume erase #4 center 2999.1,5189.7,1062.8 radius 509.95

> volume erase #4 center 2433.1,4275.4,859.06 radius 509.95

> volume erase #4 center 511.58,2336.6,234.06 radius 414.72

> volume erase #4 center 189.07,2122.9,1020.8 radius 414.72

> volume erase #4 center 2921.9,2628.5,1147.6 radius 344.06

> volume erase #4 center 2913.2,2626.7,1138.1 radius 344.06

> volume erase #4 center 3093.1,2682.3,1043.3 radius 344.06

> volume erase #4 center 2787.3,2434,1164.3 radius 344.06

[Repeated 2 time(s)]

> volume erase #4 center 2784.1,2809.1,1294.7 radius 476.16

> volume erase #4 center 2776.9,4135.3,1783.6 radius 476.16

> volume erase #4 center 2765.4,4203.7,1647.4 radius 476.16

> volume erase #4 center 2816.9,2097,1363.3 radius 476.16

> volume erase #4 center 4404.3,1191.5,1236.4 radius 476.16

> volume erase #4 center 4783.9,1246.9,1150.2 radius 476.16

> volume erase #4 center 4739.7,995.13,600.25 radius 476.16

> volume erase #4 center 3473.2,1816.6,1250.5 radius 476.16

> volume erase #4 center 1743.7,3306.3,1509.8 radius 476.16

> volume erase #4 center 2162.1,4192,672.77 radius 476.16

> volume erase #4 center 1536.5,5107,816.85 radius 476.16

> volume erase #4 center 685.47,1863.6,1277.4 radius 476.16

> volume erase #4 center 1391.2,1591.2,352.82 radius 251.9

> volume erase #4 center 1267.8,2261.5,418.88 radius 251.9

> volume erase #4 center 2716.7,2559.6,-195.85 radius 251.9

> volume erase #4 center 2726.4,2561.4,-200.73 radius 251.9

> volume erase #4 center 4685.6,933.01,625.73 radius 251.9

> volume erase #4 center 4752.9,1408.2,311.79 radius 251.9

> volume erase #4 center 4903.4,1680.5,810.28 radius 251.9

> volume erase #4 center 4820.3,1870.2,907.95 radius 251.9

> volume erase #4 center 4779.1,2132.4,873.19 radius 172.03

> volume erase #4 center 4807.3,2259.6,869.31 radius 172.03

> volume erase #4 center 4657.2,2119,857.67 radius 172.03

> volume erase #4 center 4659.7,2215.3,505.67 radius 172.03

> volume erase #4 center 3713,1035.8,538.85 radius 172.03

> volume erase #4 center 3463,1227.2,863.67 radius 172.03

> volume erase #4 center 3448,1233.7,862.24 radius 172.03

> volume erase #4 center 3386.8,1321.7,862.88 radius 172.03

> volume erase #4 center 3453.3,310.33,227.71 radius 172.03

> volume erase #4 center 2686.6,576.4,553.9 radius 147.46

> volume erase #4 center 3432.7,144.9,983.55 radius 147.46

> volume erase #4 center 4654.5,-51.12,820.61 radius 147.46

> volume erase #4 center 4718,-43.759,727.03 radius 147.46

> volume erase #4 center 4937.3,72,622.13 radius 147.46

> volume erase #4 center 4644.9,545.54,733.44 radius 147.46

> volume erase #4 center 4416.3,763.18,314.15 radius 147.46

> volume erase #4 center 3345.2,1554.4,237.87 radius 251.9

> volume erase #4 center 3343.3,960.68,877.52 radius 251.9

> volume erase #4 center 3245.5,979.03,660.03 radius 251.9

> volume erase #4 center 3252,1092.7,279.72 radius 251.9

> volume erase #4 center 3537.7,1368.1,379.31 radius 251.9

> volume erase #4 center 2373.8,3085.3,454.09 radius 251.9

> volume erase #4 center 3426.7,2778.4,321.44 radius 251.9

> volume erase #4 center 3626.2,2927.8,167.63 radius 251.9

> volume erase #4 center 2805,1158.3,893.81 radius 251.9

> volume erase #4 center 3799.4,3123.3,710.17 radius 172.03

> volume erase #4 center 3182.3,3798.6,588.35 radius 172.03

> artiax add tomo #4

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy as #2.1.1, grid size
512,512,150, pixel 12,12,12, shown at level 0.000214, step 1, values float32  

> artiax tomo #2.1.1 sliceDirection 0,0,1

> artiax view xy

> volume #2.1.1 style surface

> volume erase #2.1.1 center 2800.1,4960.8,749.97 radius 172.03

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
  
See log for complete Python traceback.  
  

> volume erase #2.1.1 center 2730.5,4927.5,775.57 radius 172.03

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
  
See log for complete Python traceback.  
  

> volume erase #2.1.1 center 2730.5,4927.5,775.57 radius 172.03

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
  
See log for complete Python traceback.  
  
Drag select of 2.1.1 PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy  

> hide #!2.1.1 models

> show #!2.1.1 models

> select clear

> open
> D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_ATP_bin1_1200.star
> format star

Summary of feedback from opening
D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_ATP_bin1_1200.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list 230213_PDC_12_ts_005_ATP_bin1_1200.star with 632
particles.  
set axis size 22.5  
22.5  
['.arrow', '0', '0', '0', '22.5', '0', '0', '1.5', '6.0']  

> artiax particles #2.2.1 originScaleFactor 1.5

> artiax view xy

> volume erase #2.1.1 center 3877.2,3613.3,1283.2 radius 500.74

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
  
See log for complete Python traceback.  
  

> volume erase #2.1.1 center 3853.5,3522.7,1223.9 radius 500.74

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
  
See log for complete Python traceback.  
  

> volume erase #2.1.1 center 3848.2,3524.2,1222.1 radius 500.74

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
  
See log for complete Python traceback.  
  

> hide #!2.2.1 models

> volume erase #2.1.1 center 4004.5,3479.9,1305.2 radius 500.74

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
  
See log for complete Python traceback.  
  

> volume erase #2.1.1 center 4004.5,3479.9,1305.2 radius 500.74

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8729
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 81TC
OS: Microsoft Windows 11 家庭中文版 (Build 22000)
Memory: 16,966,471,680
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10710U CPU @ 1.10GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    pandas: 2.0.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    starfile: 0.4.12
    superqt: 0.5.3
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Change History (3)

comment:1 by pett, 2 years ago

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

comment:2 by pett, 2 years ago

ArtiaX was also running if that's significant.

comment:3 by Tom Goddard, 2 years ago

Cc: Tom Goddard added
Owner: changed from Tom Goddard to Utz Ermel

Looks like ArtiaX is doing something not quite right in its "artiax add tomo #4" command. It then logs that it made a copy of the map as #2.1.1 and then volume eraser on that map produces the error because a volume using the same GridData as the erased one has been closed. Closing a volume by calling its delete() methods would remove the "values changed" callback. But apparently the volume was not deleted that way.

> artiax add tomo #4

Opened PDC_12_ts_005_bin8_WBP_corrected_object_1.mrc copy as #2.1.1, grid size
512,512,150, pixel 12,12,12, shown at level 0.000214, step 1, values float32  

> artiax tomo #2.1.1 sliceDirection 0,0,1

> artiax view xy

> volume #2.1.1 style surface

> volume erase #2.1.1 center 2800.1,4960.8,749.97 radius 172.03

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 322, in _erase_in_sphere  
self._erase()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 333, in _erase  
run(self.session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 28, in volume_erase  
_set_data_in_sphere(v.data, cvol, radius, value)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_eraser\eraser.py", line 47, in _set_data_in_sphere  
grid_data.values_changed()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 517, in values_changed  
self.call_callbacks('values changed')  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 531, in call_callbacks  
cb(reason)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
AttributeError: 'NoneType' object has no attribute 'clear_cache'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1378, in data_changed_cb  
self.data.clear_cache()
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