Restoring "xr true" session: SessionNotRunningError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202504030639 (2025-04-03 06:39:05 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.dev202504030639 (2025-04-03)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "D:\data\showing case\mitochodnria.cxs" format session

Opened granules as #9, grid size 512,720,127, pixel 27.2, shown at level
0.0002, step 1, values uint8  
Opened data as #17.1, grid size 512,720,127, pixel 27.2, shown at step 1,
values uint8  
Opened cristae as #2, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at
level 0.996, step 1, values int8  
Opened outer_membrane as #18, grid size 1023,1440,253, pixel 13.8,13.8,13.8,
shown at level 0.996, step 1, values int8  
Log from Wed Apr 16 12:31:04 2025UCSF ChimeraX version: 1.10.dev202504030639
(2025-04-03)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open D:\download\CM23_annotations.cxs format session

Opened granules as #9, grid size 512,720,127, pixel 27.2, shown at level
0.0002, step 1, values uint8  
Opened data as #17.1, grid size 512,720,127, pixel 27.2, shown at step 1,
values uint8  
Opened cristae as #2, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at
level 0.996, step 1, values int8  
Opened outer_membrane as #18, grid size 1023,1440,253, pixel 13.8,13.8,13.8,
shown at level 0.996, step 1, values int8  
Log from Wed Sep 18 10:11:07 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/cathyhou/Desktop/cm.cxs

Opened granules as #9, grid size 512,720,127, pixel 27.2, shown at level
0.0002, step 1, values uint8  
Opened data as #17.1, grid size 512,720,127, pixel 27.2, shown at step 1,
values uint8  
Opened cristae as #2, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at
level 0.996, step 1, values int8  
Opened outer_membrane as #18, grid size 1023,1440,253, pixel 13.8,13.8,13.8,
shown at level 0.996, step 1, values int8  
Log from Tue Sep 17 22:51:04 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/cathyhou/Desktop/cm mito.cxs"

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
as #1, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level 0.996,
step 4, values int8  
Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #3, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level
0.996, step 1, values int8  
Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #4, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level
0.996, step 1, values int8  
Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #5, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level
0.996, step 1, values int8  
Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #6, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level
0.996, step 1, values int8  
Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #8, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level
0.996, step 1, values int8  
Opened granules as #9, grid size 512,720,127, pixel 27.2, shown at level
0.0002, step 1, values uint8  
Opened volume difference as #10, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at level 0.996, step 1, values int8  
Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #11, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level
0.996, step 1, values int8  
Opened volume difference as #12, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at level 0.996, step 1, values int8  
Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #13, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level
0.996, step 1, values int8  
Opened volume difference as #14, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at level 0.996, step 1, values int8  
Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #15, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at level
0.996, step 1, values int8  
Opened volume difference as #16, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at level 0.996, step 1, values int8  
Opened data as #17.1, grid size 512,720,127, pixel 27.2, shown at step 1,
values uint8  
Opened cristae as #2, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at
level 0.996, step 1, values int8  
Opened outer_membrane as #18, grid size 1023,1440,253, pixel 13.8,13.8,13.8,
shown at level 0.996, step 1, values int8  
Log from Tue Sep 17 22:46:54 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/cathyhou/Downloads/20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
as #1, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1, values
int8  

> volume #1 region 0,0,0,1022,1439,252 step 4

[Repeated 1 time(s)]

> volume #1 change image level 0,0 level 0.1,0.8 level 1,1

> volume #1 level 0.9964

> ui tool show "Map Eraser"

> volume erase #1 center 1635.6,1657.4,-5.846 radius 2436.1

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #3, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1,
values int8  

> volume erase #3 center 11389,10667,1676.9 radius 2575.9 outside true

> volume erase #3 center 15801,8840.6,627.51 radius 2575.9

> volume erase #3 center 15957,8799,1883.2 radius 2575.9

> volume erase #3 center 16219,9601.4,2118.2 radius 2575.9

> volume erase #3 center 13501,6269.3,1358.5 radius 2575.9

> volume erase #3 center 13826,7035,-56.643 radius 2575.9

> volume erase #3 center 10293,6397.8,-394.46 radius 2575.9

> volume erase #3 center 8441.4,7088.5,135.58 radius 2575.9

> volume erase #3 center 7249.7,8364.6,968.59 radius 2575.9

> volume erase #3 center 6690.9,9975.8,1685.1 radius 2575.9

> volume erase #3 center 8139.6,13653,2358.7 radius 2575.9

> volume erase #3 center 8015.4,13610,1688.3 radius 2575.9

> volume erase #3 center 7261.9,12751,1802.2 radius 2575.9

> volume erase #3 center 11661,14885,3476.7 radius 2575.9

> volume erase #3 center 13442,13677,4411.5 radius 2575.9

> volume erase #3 center 14950,11480,4589.3 radius 2575.9

> volume erase #3 center 15754,12628,1468.4 radius 2575.9

> volume erase #3 center 14696,14163,1723.2 radius 2575.9

> volume erase #3 center 13923,6622,2175.4 radius 2575.9

> volume erase #3 center 13278,6403.6,2252.4 radius 2575.9

> volume erase #3 center 11830,6998.7,4095.9 radius 2575.9

> volume erase #3 center 10234,7021.2,3871.1 radius 2575.9

> volume erase #1 center 8437.8,13220,1725.9 radius 2576 outside true

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #4, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1,
values int8  

> volume erase #4 center 4127.4,14388,1217.3 radius 2576

> volume erase #4 center 4100.2,14045,2520.3 radius 2576

> volume erase #4 center 4279.6,11543,1738.3 radius 2576

> volume erase #4 center 5014.6,10432,1353 radius 2576

> volume erase #4 center 4620.1,11049,1531.9 radius 2576

> volume erase #4 center 7624.1,8552,2029.4 radius 2576

> volume erase #4 center 7431.4,8861.2,3351.3 radius 2576

> volume erase #4 center 7979.8,8603.7,540.53 radius 2576

> volume erase #4 center 7518.2,12829,-1890.8 radius 2576

> volume erase #4 center 11776,10136,1146.9 radius 2576

> volume erase #4 center 11684,10004,1810.3 radius 2576

> volume erase #4 center 12149,10495,1586 radius 2576

> volume erase #4 center 11836,16260,2507.9 radius 2576

> volume erase #4 center 10968,16856,1362.8 radius 2576

> volume erase #4 center 9334.1,17556,1783.9 radius 2576

> volume erase #4 center 7989.1,17645,2045.4 radius 2576

> volume erase #4 center 8927.5,10716,-1545.4 radius 2576

> volume erase #4 center 12950,13617,3198.6 radius 2576

> volume erase #4 center 8421.7,11483,1802.6 radius 346.75

> volume erase #3 center 10945,11803,2550.7 radius 346.75

> volume erase #3 center 10979,11855,2362.4 radius 346.75

> volume erase #3 center 11156,11952,2332 radius 346.75

> volume erase #3 center 11137,11946,2336.2 radius 346.75

> volume erase #3 center 11120,11927,2499.4 radius 346.75

> volume erase #3 center 11143,11948,2408.3 radius 346.75

> volume erase #3 center 11138,11976,2359.4 radius 346.75

> volume erase #1 center 5156.7,10942,915.61 radius 2903 outside true

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #5, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1,
values int8  

> volume erase #5 center 10087,9270.5,1586.8 radius 2903

> volume erase #5 center 9365.3,13746,1575.8 radius 2903

> volume erase #5 center 9418.1,13659,1936.1 radius 2903

> volume erase #5 center 9731.6,13238,1743.3 radius 2903

> volume erase #5 center 9700.7,13173,1737.7 radius 2903

> volume erase #5 center 10302,10253,1847.3 radius 2903

> volume erase #5 center 6883.6,15460,3377.4 radius 2903

> volume erase #5 center 8968.4,14333,2333.1 radius 2903

> volume erase #5 center 6158.9,15852,68.942 radius 2903

> volume erase #5 center 6998.1,12599,-2344.5 radius 2903

> volume erase #5 center 4611.1,16131,2305.1 radius 2903

> volume erase #5 center 4541.1,16104,1800.8 radius 2903

> volume erase #5 center 1507.5,14981,1441.7 radius 2903

> volume erase #5 center 587.33,13935,1241.7 radius 2903

> volume erase #5 center 899.38,14299,914.19 radius 2903

> volume erase #5 center 443.79,13566,2277.5 radius 2903

> volume erase #5 center 1047.2,14293,2643.2 radius 2903

> volume erase #5 center 1929.9,15051,3016.9 radius 2903

> volume erase #5 center -150.56,10701,1301.8 radius 2903

> volume erase #5 center 2198.3,7112.2,63.553 radius 2903

> volume erase #5 center 3513.4,6296.1,559.18 radius 2903

> volume erase #5 center 3727.9,8858.3,4844.1 radius 2903

> volume erase #5 center 4510.6,5606.9,2689.2 radius 2903

> volume erase #5 center 5706,5808.1,905.82 radius 2903

> volume erase #5 center 4937.7,6376.5,-523.04 radius 2903

> volume erase #5 center 2934.1,6737.4,-57.823 radius 2903

> volume erase #5 center 1925.5,7077.8,741.19 radius 2903

> volume erase #5 center 2714.5,6418.8,1206.2 radius 2903

> volume erase #5 center 6404.9,6453.8,3433.4 radius 2903

> volume erase #5 center 8084.4,6972.5,3145.2 radius 2903

> volume erase #5 center 5560.3,8855.3,2434.3 radius 435.92

> volume erase #5 center 5132,9221.5,2197.7 radius 435.92

> volume erase #5 center 5561.5,8992.7,1941.4 radius 237.77

> volume erase #5 center 4257.3,9578.5,2076 radius 237.77

> volume erase #5 center 5214.4,8885.7,2318.5 radius 237.77

> volume erase #5 center 5246.2,8910.1,2136 radius 237.77

> volume erase #5 center 5377.3,8897.6,2051.1 radius 237.77

> volume erase #5 center 5330,8931.7,1991.5 radius 237.77

> volume erase #5 center 5842.6,8861,1873 radius 128.79

> volume erase #5 center 5422.9,8807.6,1770.4 radius 69.35

> volume erase #5 center 5971.7,8771.8,1759.2 radius 69.35

> volume erase #5 center 6053.6,8754,1747.9 radius 69.35

> volume erase #5 center 5450.1,8757.7,1866.9 radius 69.35

> volume erase #5 center 5516.8,8756,1809.2 radius 69.35

> volume erase #5 center 4526.6,6487.1,1333.4 radius 2338.1

> volume erase #5 center 2744.5,7137.9,1532.3 radius 2338.1

> volume erase #5 center 3443.3,6877.2,1368.4 radius 2338.1

> volume erase #1 center 1716.6,13382,1371.2 radius 2843.4 outside true

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #6, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1,
values int8  

> volume erase #6 center 1804.7,9002.3,563.78 radius 2833.5

> volume erase #6 center 5742.7,15401,1886.7 radius 2833.5

> volume erase #6 center 5456.5,10893,1123.4 radius 2833.5

> volume erase #6 center 5213,10520,1538 radius 2833.5

> volume erase #6 center 2720,8759.8,1890 radius 2833.5

> volume erase #6 center 3119.4,17607,321.4 radius 2833.5

> volume erase #6 center -61.943,16280,-48.682 radius 2833.5

> volume erase #6 center 412.45,17290,2895.8 radius 2833.5

> volume erase #6 center 3770.4,17148,3291.7 radius 2833.5

> volume erase #6 center 3759.7,17443,1810.2 radius 2833.5

> volume erase #6 center 4743.3,16447,3082.4 radius 2833.5

> volume erase #6 center 2630.7,15064,5293.2 radius 2833.5

> volume erase #6 center 665.54,11029,5019.6 radius 2833.5

> volume erase #6 center -1244.4,14569,3232.9 radius 2833.5

> save "/Users/cathyhou/Desktop/cm mito.cxs" includeMaps true

> volume erase #6 center 1688.2,10197,1231 radius 1575.2

> volume erase #6 center 1482.1,10266,1235.3 radius 1575.2

> volume erase #6 center -243.1,9908.4,1348.4 radius 1575.2

> volume erase #6 center 1211.8,10152,1318.2 radius 1575.2

> volume erase #6 center -11.282,10082,592.59 radius 1575.2

> volume erase #6 center -26.024,10100,583.21 radius 1575.2

> volume erase #6 center 452.95,10181,451.61 radius 1575.2

> volume erase #6 center 1288.8,10506,288.56 radius 1575.2

> volume erase #6 center 1482.6,10280,1130.8 radius 1575.2

> volume erase #6 center 1476.8,10216,1495.8 radius 1575.2

> volume erase #6 center 1494.4,11535,1162.3 radius 455.73

> volume erase #6 center 1462.4,11399,1562.5 radius 455.73

> volume erase #6 center 1366.8,11561,1019.2 radius 455.73

> ui tool show "Hide Dust"

> surface dust #3 size 82.56

> surface dust #3 size 79.71

> surface dust #3 size 4182.3

> surface dust #3 size 4284.7

> surface dust #3 size 114.87

> surface dust #3 size 113.53

> surface dust #3 size 13.76

> save "/Users/cathyhou/Desktop/cm mito.cxs" includeMaps true

> open /Users/cathyhou/Downloads/20230113_RCG_CM_tomo00023_bin4_filtered.hdf

Opened data as #7.1, grid size 512,720,127, pixel 1, shown at level 219, step
2, values uint8  
Opened label as #7.2, grid size 512,720,127, pixel 1, shown at level 0.0002,
step 2, values int8  
Opened preds as #7.3, grid size 512,720,127, pixel 1, shown at level 255, step
2, values uint8  

> hide #!7.2 models

> volume #7.3 level 0.0002

> ui tool show "Map Coordinates"

> volume copy #3

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #8, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1,
values int8  

> close #7.2

> ui tool show "Map Coordinates"

> volume #7.1 style image region 0,0,62,511,719,62 step 1 showOutlineBox true

> close #7.1

> volume #7.3 region 0,0,0,511,719,126

[Repeated 7 time(s)]

> ui tool show "Map Eraser"

> volume erase #7.3 center 5013.3,5737.2,2272.6 radius 2419.9

Opened preds copy as #9, grid size 512,720,127, pixel 27.2, shown at step 1,
values uint8  

> volume erase #9 center 725.15,8597.3,2047.1 radius 2418.6

> volume erase #9 center -157.05,-805.35,1807.9 radius 2418.6

> volume erase #9 center 85.917,19138,1864.4 radius 2418.6

> volume erase #9 center 12907,1513,-4432.4 radius 4572.9

> volume erase #9 center 12622,1826.7,896.66 radius 4572.9

> volume erase #9 center 7501.1,6659.2,77.884 radius 714.82

[Repeated 1 time(s)]

> volume erase #9 center 6426,8432.8,1269.6 radius 714.82

> volume erase #9 center 8844.1,11252,280.9 radius 714.82

> volume erase #9 center 14323,19991,3265.7 radius 714.82

> volume erase #9 center 14030,19468,187.77 radius 714.82

> volume erase #9 center 8293,12084,3569.3 radius 714.82

> close #7.3

> volume erase #8 center 11285,10228,1723.4 radius 1654.5 outside true

> volume erase #8 center 12768,7834.9,647.9 radius 1654.5

> volume erase #8 center 11097,7677.3,657.4 radius 1654.5

> volume erase #8 center 9368.2,7747.2,1263.1 radius 1654.5

> volume erase #8 center 9533.2,8537.6,271 radius 1654.5

> volume erase #8 center 12697,9926.1,-976.65 radius 1654.5

> volume #8 color #48bfb5

> volume #8 color #00fdff

> volume #3 color #0433ff

> volume subtract #8 #3

Opened volume difference as #10, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at step 1, values int8  

> close #10

> volume subtract #3 #8

Opened volume difference as #10, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at step 1, values int8  

> volume erase #10 center 11773,10679,116.54 radius 356.66

> volume #3 color #b2b2b2

> volume #10 color #0433ff

> volume copy #4

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #11, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1,
values int8  

> volume erase #11 center 8488.5,13048,1681.4 radius 1674.3 outside true

> volume erase #11 center 5645.1,12182,1004.6 radius 1674.3

> volume erase #11 center 6587.3,11147,1362.8 radius 1674.3

> volume erase #11 center 6317.5,11188,1171.8 radius 1674.3

> volume erase #11 center 6041.9,11664,1125.9 radius 1674.3

> volume erase #11 center 10249,10495,2174.9 radius 1674.3

> volume erase #11 center 11081,11260,1156.8 radius 1674.3

> volume erase #11 center 10559,10688,1492.7 radius 1674.3

> volume erase #11 center 10685,12259,-436.67 radius 1674.3

> volume erase #11 center 10332,11165,-155.34 radius 1674.3

> volume erase #11 center 11001,14123,116.93 radius 1674.3

> volume #11 color #00fdff

> volume subtract #4 #11

Opened volume difference as #12, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at step 1, values int8  

> volume #12 color #0433ff

> volume copy #5

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #13, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1,
values int8  

> volume erase #13 center 5098.1,11179,1291.2 radius 2199.4 outside true

> volume erase #13 center 2838.7,14205,1534.4 radius 2199.4

> volume erase #13 center 1709.7,11591,134.11 radius 2199.4

> volume erase #13 center 3506.9,8506.8,-302.51 radius 2199.4

> volume erase #13 center 8373,12919,3094.8 radius 2199.4

> volume erase #13 center 6168.8,14892,1924.2 radius 2031

> volume erase #13 center 7388.5,14313,2140.9 radius 2031

[Repeated 1 time(s)]

> volume erase #13 center 7421.3,14027,2522.3 radius 2031

> volume erase #13 center 6761.6,14500,2815.3 radius 2031

> volume erase #13 center 6258.4,7725.5,-187.47 radius 2031

> volume erase #13 center 7678.3,9395.5,-738.75 radius 2031

> volume erase #13 center 8236.3,9144.1,181.51 radius 2031

> volume erase #13 center 6205.5,10087,-1634.3 radius 2031

> volume erase #13 center 7795.2,12901,192.07 radius 2031

> volume erase #13 center 8355.3,11428,287.17 radius 2031

> volume erase #13 center 7606.1,10636,2304.2 radius 713.32

> volume erase #13 center 7547.9,11195,2780 radius 713.32

> volume erase #13 center 7441.4,11415,2858.4 radius 713.32

> volume erase #13 center 7618.2,11392,2617.8 radius 713.32

> volume erase #13 center 7819.8,11529,2147.4 radius 713.32

> volume erase #13 center 7720.7,11033,1897.9 radius 713.32

> volume erase #13 center 7077.8,12261,1882.7 radius 713.32

> volume erase #13 center 7176.1,11906,2515.2 radius 713.32

> volume erase #13 center 7475.1,11877,1751.4 radius 713.32

> volume #13 color #00fdff

> volume subtract #5 #13

Opened volume difference as #14, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at step 1, values int8  

> volume #14 color #0433ff

> volume erase #14 center 5085.9,12468,1821.6 radius 713.32

> volume erase #13 center 5519.7,12934,2207.2 radius 138.7

> volume copy #6

Opened
20230113_RCG_CM_tomo00023_bin4_filtered_MemBrain_seg_v10_alpha.ckpt_segmented.mrc
copy as #15, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown at step 1,
values int8  

> volume erase #15 center 1484.4,13679,1739.7 radius 1347.4

> volume erase #15 center 428.49,13273,1711.7 radius 1347.4

> volume erase #15 center 526.95,13497,1194.4 radius 1347.4

> volume erase #15 center -558.06,12033,3755.9 radius 1347.4

> volume erase #15 center -110.4,10320,2820.6 radius 1347.4

> volume erase #15 center 2462.5,13288,2241.8 radius 852.02

> volume erase #15 center 1915.4,13931,1119.5 radius 852.02

> volume erase #15 center 1929.9,13058,1068.9 radius 852.02

> volume erase #15 center 2231.2,12747,1904.4 radius 544.9

> volume erase #15 center 2826.8,13273,1588.2 radius 544.9

> volume erase #15 center 2049.9,12500,2028.1 radius 544.9

> volume erase #15 center 2014.3,12459,2155.9 radius 544.9

> volume erase #15 center 2777.5,13273,1499.5 radius 544.9

> volume erase #15 center 2807.6,13274,1407.8 radius 544.9

> volume erase #15 center 3341.1,13198,2253.5 radius 168.42

> volume erase #15 center 3261.5,13373,2359 radius 168.42

> volume erase #15 center 3320.1,13243,2387.6 radius 168.42

> volume erase #15 center 3306.1,13394,2411.1 radius 168.42

> volume erase #15 center 3328.5,13289,2391 radius 168.42

> volume subtract #15 #6

Opened volume difference as #16, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at step 1, values int8  

> close #16

> volume subtract #6 #15

Opened volume difference as #16, grid size 1023,1440,253, pixel
13.8,13.8,13.8, shown at step 1, values int8  

> volume erase #16 center -165.47,10962,2466.4 radius 544.9

> volume erase #16 center 114.19,10958,2038.4 radius 544.9

> volume erase #16 center 772.47,12167,2278.6 radius 544.9

> volume erase #16 center 808.35,13867,2050.3 radius 544.9

> volume erase #16 center 928.03,12168,689.25 radius 544.9

> volume erase #16 center 1298,12840,525.97 radius 544.9

> volume erase #16 center 1802.2,14719,577.6 radius 544.9

> volume erase #16 center 2492.4,14796,2251.1 radius 544.9

> volume erase #16 center 2622.5,14601,2489.3 radius 544.9

> volume erase #16 center 3334,13380,888.36 radius 544.9

> volume erase #16 center 2629.3,12441,710.91 radius 544.9

> volume erase #16 center 2810.3,11945,2251.9 radius 544.9

> volume #16 color #00fdff

> volume #15 color #0433ff

> open /Users/cathyhou/Downloads/20230113_RCG_CM_tomo00023_bin4_filtered.hdf

Opened data as #17.1, grid size 512,720,127, pixel 1, shown at level 219, step
2, values uint8  
Opened label as #17.2, grid size 512,720,127, pixel 1, shown at level 0.0002,
step 2, values int8  
Opened preds as #17.3, grid size 512,720,127, pixel 1, shown at level 255,
step 2, values uint8  

> close #17.3

> close #17.2

> ui tool show "Map Coordinates"

> volume #17.1 style image region 0,0,62,511,719,62 step 1 showOutlineBox true

> volume #17.1 color white color #ffffbf color #ffffbf

> volume #17.1 level 74.01,0 level 179.7,0.9231 level 255,1

> hide #!16 models

> hide #!15 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!13 models

> hide #!14 models

> volume #16 region 0,0,0,1022,1439,252

[Repeated 2 time(s)]

> ui tool show "Map Eraser"

> ui tool show "Hide Dust"

> surface dust #16 size 82.56

[Repeated 1 time(s)]

> surface dust #16 size 88.6

> surface dust #16 size 351.98

> volume add #16,13,11,8

Opened volume sum as #2, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown
at step 1, values int8  

> volume add #15,14,12,10

Opened volume sum as #18, grid size 1023,1440,253, pixel 13.8,13.8,13.8, shown
at step 1, values int8  

> volume #18 color #0433ff

> set bgColor white

> set bgColor black

> rename #18 outer_membrane

> rename #2 cristae

> ui tool show "Hide Dust"

> surface dust #2 size 82.56

> surface dust #2 size 81.61

> surface dust #2 size 309.11

> surface dust #2 size 30

> surface dust #2 size 300

[Repeated 1 time(s)]

> surface dust #18 size 82.56

> surface dust #18 size 30

> surface dust #18 size 300

[Repeated 1 time(s)]

> volume #9 color #0433ff

> volume #2 color #00fdff

> volume #18 color #fffb00

> set bgColor white

> volume #9 color #ebeced

> volume #9 color #0d17cc

> rename #9 granules

> volume #2 color #4eabe7

> volume #18 color #ffff54

> volume #2 color #cafcfc

> volume #2 color #80fcfd

> volume #18 color #ffff5d

> volume #9 color #0101ec

> save /Users/cathyhou/Desktop/cm.mrc #2,9,18,17.1

> save "/Users/cathyhou/Desktop/cm mito.cxs" includeMaps true

——— End of log from Tue Sep 17 22:46:54 2024 ———

opened ChimeraX session  

> save /Users/cathyhou/Desktop/cm.mrc #2,9,18

Cannot write multiple volumes using format mrc  

> save /Users/cathyhou/Desktop/cm.cxs #2,9,18,17

Expected a keyword  

> save /Users/cathyhou/Desktop/cm.cxs #2,9,18,17.1

Expected a keyword  

> close #1

> close #3

> close #4

> close #5

> close #6

> close #8

> close #10

> close #11

> close #12

> close #13

> close #14

> close #15

> close #16

> hide #7 models

> show #7 models

> hide #7 models

> close #7

> save /Users/cathyhou/Desktop/cm.cxs includeMaps true

——— End of log from Tue Sep 17 22:51:04 2024 ———

opened ChimeraX session  

> set bgColor black

> view orient

> save /Users/cathyhou/Desktop/cm.cxs includeMaps true

——— End of log from Wed Sep 18 10:11:07 2024 ———

> view name session-start

opened ChimeraX session  

> xr true

> mousemode setting zoom speed 0.2

started OpenXR rendering SonySRD System, render size 3840 by 2160  

> ui mousemode right pivot

> ui mousemode right translate

> save "D:/data/showing case/mitochodnria.cxs"

——— End of log from Wed Apr 16 12:31:04 2025 ———

> mousemode setting zoom speed 0.2

started OpenXR rendering SonySRD System, render size 3840 by 2160  

> view name session-start

opened ChimeraX session  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
The session <<session-not-running, is not yet running>>.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\graphics\view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\graphics\view.py", line 231, in _draw_scene  
camera.set_render_target(vnum, r)  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\vive\xr.py", line 1140, in set_render_target  
self._start_rendering()  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\vive\xr.py", line 958, in _start_rendering  
if not xr.start_frame():  
^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\vive\openxr.py", line 378, in start_frame  
self._poll_xr_events()  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\vive\openxr.py", line 410, in _poll_xr_events  
self._on_session_state_changed(event_buffer)  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\vive\openxr.py", line 432, in _on_session_state_changed  
self.shutdown()  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\chimerax\vive\openxr.py", line 766, in shutdown  
xr.request_exit_session(self._session)  
File "C:\Program Files\ChimeraX 1.10.dev202504030639\bin\Lib\site-
packages\xr\functions.py", line 639, in request_exit_session  
raise result  
xr.exception.SessionNotRunningError: The session <<session-not-running, is not
yet running>>.  
  




OpenGL version: 3.3.0 NVIDIA 572.76
OpenGL renderer: NVIDIA GeForce RTX 4090 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision 7780
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 68,388,900,864
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13950HX
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    autocommand: 2.2.2
    babel: 2.17.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.2.1
    build: 1.2.2.post1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202504030639
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.3
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.8
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.1
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    inflect: 7.3.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.collections: 5.1.0
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    platformdirs: 4.2.2
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 26.3.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.13.0
    typing_extensions: 4.12.2
    tzdata: 2025.2
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel: 0.43.0
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    zipp: 3.19.2

[Tom Goddard]

User saved a session while using OpenXR with a Sony 3D display. Later opening that session gave an error that the Sony display was not ready when it tried to start OpenXR. Maybe the session should remember OpenXR camera settings but not try to restart it. But if they saved the session intentionally to save the same Sony 3D view it seems sensible to try to restore that. Not sure why the display says

xr.exception.SessionNotRunningError: The session <<session-not-running, is not

yet running>>.

Should try restoring session with Sony no longer connected.

The error happens when OpenXR is trying to shutdown the openxr session. Maybe we should just catch that error, warn, and close the openxr.

[Tom Goddard]

Was reported a second time by the same user #17508