id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17507	"Restoring ""xr true"" session: SessionNotRunningError"	chimerax-bug-report@…	Tom Goddard	"{{{
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
}}}
"	defect	assigned	normal		Sessions								all	ChimeraX