ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/FUS/map/1 postprocess_masked.mrc" "D:/FUS/map/2
> postprocess_masked.mrc"

Opened 1 postprocess_masked.mrc as #1.1, grid size 360,360,360, pixel 0.83,
shown at level 0.00268, step 2, values float32  
Opened 2 postprocess_masked.mrc as #1.2, grid size 360,360,360, pixel 0.83,
shown at level 0.00232, step 2, values float32  

> select add #1.1

2 models selected  

> select add #1

5 models selected  

> select add #1.2

5 models selected  

> select subtract #1.1

3 models selected  

> select subtract #1.2

1 model selected  

> select add #1.2

3 models selected  

> select subtract #1

Nothing selected  

> select subtract #1.2

Nothing selected  

> select add #1

5 models selected  

> show target m

> select subtract #1

Nothing selected  

> close #1.1-2

> close

> open "D:/FUS/map/1 postprocess_masked.mrc"

Opened 1 postprocess_masked.mrc as #1, grid size 360,360,360, pixel 0.83,
shown at level 0.00268, step 2, values float32  

> open "D:/FUS/map/1 postprocess_masked.mrc"

Opened 1 postprocess_masked.mrc as #2, grid size 360,360,360, pixel 0.83,
shown at level 0.00268, step 2, values float32  

> set bgColor white

> volume #1 step 1

> volume #2 step 1

> surface dust #1 size 8.3

> surface dust #2 size 8.3

> select add #1

2 models selected  

> select add #2

4 models selected  

> select subtract #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-0.50591,0,1,0,1.5243,0,0,1,-27.125

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99814,-0.06098,-0.0027381,10.003,0.060983,0.99814,0.00083898,-7.0922,0.0026818,-0.0010044,1,-27.349

> fitmap #1 inMap #2

Fit map 1 postprocess_masked.mrc in map 1 postprocess_masked.mrc using 466122
points  
correlation = 0.4606, correlation about mean = 0.2832, overlap = 27.96  
steps = 80, shift = 2.53, angle = 1.28 degrees  
  
Position of 1 postprocess_masked.mrc (#1) relative to 1 postprocess_masked.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99924853 -0.03875574 -0.00060823 5.99664513  
0.03875602 0.99924859 0.00046486 -5.75976826  
0.00058976 -0.00048808 0.99999971 -28.94412208  
Axis -0.01229166 -0.01545252 0.99980505  
Axis point 162.90892987 142.39723081 0.00000000  
Rotation angle (degrees) 2.22153801  
Shift along axis -28.92318514  
  

> vop add #1 #2

Opened volume sum as #3, grid size 376,376,397, pixel 0.83, shown at step 1,
values float32  

> select subtract #1

Nothing selected  

> show #!1 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> close #1-3

> open D:/FUS/map/1fl-postprocess_masked.mrc

Opened 1fl-postprocess_masked.mrc as #1, grid size 360,360,360, pixel 0.83,
shown at level 0.0195, step 2, values float32  

> volume #1 step 1

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> open D:/FUS/map/1fl-postprocess_masked.mrc

Opened 1fl-postprocess_masked.mrc as #2, grid size 360,360,360, pixel 0.83,
shown at level 0.0195, step 2, values float32  

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,2.01,0,1,0,1.0956,0,0,1,-70.623

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.97241,-0.23322,0.0049349,42.859,0.23314,0.97235,0.013201,-29.317,-0.0078773,-0.011687,0.9999,-67.607

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97241,-0.23322,0.0049349,43.895,0.23314,0.97235,0.013201,-28.624,-0.0078773,-0.011687,0.9999,-105.73

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.97404,-0.22423,-0.031107,47.564,0.22469,0.97435,0.012301,-27.62,0.027551,-0.018972,0.99944,-109.48

> view matrix models
> #2,0.97415,-0.22545,-0.014357,45.258,0.2251,0.97408,-0.022383,-22.483,0.019031,0.018572,0.99965,-114.38

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97415,-0.22545,-0.014357,50.791,0.2251,0.97408,-0.022383,-21.85,0.019031,0.018572,0.99965,-161.79

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87385,-0.48427,-0.043208,111.06,0.48415,0.87487,-0.013902,-43.657,0.044534,-0.0087712,0.99897,-160.87

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.87385,-0.48427,-0.043208,119.32,0.48415,0.87487,-0.013902,-41.43,0.044534,-0.0087712,0.99897,-236.5

> view matrix models
> #2,0.87385,-0.48427,-0.043208,106.75,0.48415,0.87487,-0.013902,-45.324,0.044534,-0.0087712,0.99897,-241.17

> view matrix models
> #2,0.87385,-0.48427,-0.043208,104.22,0.48415,0.87487,-0.013902,-46.441,0.044534,-0.0087712,0.99897,-241.14

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87856,-0.47758,0.0068468,95.036,0.47758,0.87859,0.0018762,-48.457,-0.0069115,0.0016215,0.99997,-235.71

> view matrix models
> #2,0.878,-0.47866,0.0018663,96.031,0.47855,0.8777,-0.025248,-44.422,0.010447,0.023061,0.99968,-241.58

> view matrix models
> #2,0.87813,-0.47774,0.025449,92.361,0.47812,0.87823,-0.010958,-46.568,-0.017115,0.02179,0.99962,-237.47

> view matrix models
> #2,0.97079,-0.23951,0.013984,42.484,0.23964,0.97082,-0.0086093,-28.208,-0.011514,0.011709,0.99987,-236.67

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97079,-0.23951,0.013984,38.817,0.23964,0.97082,-0.0086093,-31.105,-0.011514,0.011709,0.99987,-236.47

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit map 1fl-postprocess_masked.mrc in map 1fl-postprocess_masked.mrc using
58317 points  
correlation = 0.2941, correlation about mean = -0.1467, overlap = 3.618  
steps = 456, shift = 1.6, angle = 4.5 degrees  
  
Position of 1fl-postprocess_masked.mrc (#2) relative to 1fl-
postprocess_masked.mrc (#1) coordinates:  
Matrix rotation and translation  
0.94999639 -0.31223914 -0.00368588 55.05316242  
0.31225092 0.94999421 0.00322065 -40.01774346  
0.00249595 -0.00421052 0.99998802 -237.19241841  
Axis -0.01189815 -0.00989782 0.99988023  
Axis point 158.40981953 141.90150669 0.00000000  
Rotation angle (degrees) 18.19683430  
Shift along axis -237.42295150  
  

> vop add #1 #2

Opened volume sum as #3, grid size 458,457,649, pixel 0.83, shown at step 1,
values float32  

> select subtract #2

Nothing selected  

> hide #!3 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #!1 models

> fitmap #2 inMap #1

Fit map 1fl-postprocess_masked.mrc in map 1fl-postprocess_masked.mrc using
58317 points  
correlation = 0.2941, correlation about mean = -0.1466, overlap = 3.618  
steps = 2000, shift = 0.107, angle = 0.0586 degrees  
  
Position of 1fl-postprocess_masked.mrc (#2) relative to 1fl-
postprocess_masked.mrc (#1) coordinates:  
Matrix rotation and translation  
0.94998360 -0.31228042 -0.00347856 54.99020667  
0.31229348 0.94997630 0.00422089 -40.26974608  
0.00198644 -0.00509611 0.99998504 -236.98426583  
Axis -0.01491515 -0.00874866 0.99985049  
Axis point 157.93787073 139.45676358 0.00000000  
Rotation angle (degrees) 18.19992350  
Shift along axis -237.41671475  
  

> vop add #1 #2

Opened volume sum as #4, grid size 457,458,649, pixel 0.83, shown at step 1,
values float32  

> close #3

> surface dust #4 size 8.3

> volume #2 step 1

> hide #!4 models

> show #!1 models

> fitmap #2 inMap #1

Fit map 1fl-postprocess_masked.mrc in map 1fl-postprocess_masked.mrc using
466035 points  
correlation = 0.2942, correlation about mean = -0.1424, overlap = 28.83  
steps = 276, shift = 0.0649, angle = 0.0383 degrees  
  
Position of 1fl-postprocess_masked.mrc (#2) relative to 1fl-
postprocess_masked.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95000571 -0.31221144 -0.00362945 55.03151100  
0.31222383 0.95000185 0.00357324 -40.11234919  
0.00233238 -0.00452780 0.99998703 -237.13444407  
Axis -0.01297170 -0.00954632 0.99987029  
Axis point 158.31933814 141.04709587 0.00000000  
Rotation angle (degrees) 18.19536912  
Shift along axis -237.43461297  
  

> vop add #1 #2

Opened volume sum as #3, grid size 458,457,649, pixel 0.83, shown at step 1,
values float32  

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!3 models

> close #3-4

> vop add #1 #2

Opened volume sum as #3, grid size 458,457,649, pixel 0.83, shown at step 1,
values float32  

> volume #3 level 0.0139

> close #3

> vop maximum #1 #2

Opened volume maximum as #3, grid size 458,457,649, pixel 0.83, shown at step
1, values float32  

> hide #!3 models

> show #!3 models

> vop maximum #1 #2

Opened volume maximum as #4, grid size 458,457,649, pixel 0.83, shown at step
1, values float32  

> select add #4

2 models selected  

> view matrix models #4,1,0,0,-4.8803,0,1,0,3.292,0,0,1,-113.56

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.96976,-0.24123,0.037135,36.402,0.24327,0.96766,-0.066779,-23.396,-0.019825,0.073794,0.99708,-122.4

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.96976,-0.24123,0.037135,30.115,0.24327,0.96766,-0.066779,-17.417,-0.019825,0.073794,0.99708,-299.44

> view matrix models
> #4,0.96976,-0.24123,0.037135,24.115,0.24327,0.96766,-0.066779,-7.0937,-0.019825,0.073794,0.99708,-461.14

> view matrix models
> #4,0.96976,-0.24123,0.037135,27.584,0.24327,0.96766,-0.066779,-12.869,-0.019825,0.073794,0.99708,-462.3

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.85931,-0.49721,0.11984,80.981,0.50315,0.86388,-0.023637,-33.839,-0.091774,0.080608,0.99251,-453.25

> view matrix models
> #4,0.86041,-0.50193,0.088073,82.527,0.50152,0.86468,0.028397,-35.295,-0.090408,0.019737,0.99571,-443.89

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.86041,-0.50193,0.088073,85.163,0.50152,0.86468,0.028397,-59.977,-0.090408,0.019737,0.99571,-441.61

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.86244,-0.50197,0.064943,85.577,0.4994,0.86479,0.052323,-60.414,-0.082427,-0.012693,0.99652,-437.61

> view matrix models
> #4,0.85966,-0.51082,0.0074625,89.082,0.51078,0.85969,0.0062147,-59.81,-0.00959,-0.0015308,0.99995,-449.6

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.85966,-0.51082,0.0074625,92.979,0.51078,0.85969,0.0062147,-62.11,-0.00959,-0.0015308,0.99995,-449.33

> fitmap #4 inMap #3

Fit map volume maximum in map volume maximum using 832367 points  
correlation = 0.3042, correlation about mean = -0.06039, overlap = 48.57  
steps = 2000, shift = 7.34, angle = 3.87 degrees  
  
Position of volume maximum (#4) relative to volume maximum (#3) coordinates:  
Matrix rotation and translation  
0.82388197 -0.56674472 -0.00434924 113.07062923  
0.56675694 0.82388169 0.00235099 -59.62493542  
0.00225085 -0.00440190 0.99998778 -450.22360112  
Axis -0.00595735 -0.00582254 0.99996530  
Axis point 155.35546833 146.49583432 0.00000000  
Rotation angle (degrees) 34.52532809  
Shift along axis -450.53441223  
  

> fitmap #4 inMap #3

Fit map volume maximum in map volume maximum using 832367 points  
correlation = 0.3044, correlation about mean = -0.06281, overlap = 48.18  
steps = 2000, shift = 1.11, angle = 0.246 degrees  
  
Position of volume maximum (#4) relative to volume maximum (#3) coordinates:  
Matrix rotation and translation  
0.82383182 -0.56677890 -0.00792566 113.82374451  
0.56682124 0.82382723 0.00472929 -60.60296097  
0.00384891 -0.00838857 0.99995741 -450.11955906  
Axis -0.01157046 -0.01038563 0.99987912  
Axis point 159.34107616 142.09685863 0.00000000  
Rotation angle (degrees) 34.53215045  
Shift along axis -450.75274381  
  

> select subtract #4

Nothing selected  

> select add #4

2 models selected  

> select subtract #4

Nothing selected  

> vop maximum #3 #4

Opened volume maximum as #5, grid size 643,641,1197, pixel 0.83, shown at step
1, values float32  

> save D:/FUS/halfpitch_HC/donor1.cxs

> vop maximum #3 #4

Opened volume maximum as #6, grid size 643,641,1197, pixel 0.83, shown at step
1, values float32  

> select add #6

2 models selected  

> view matrix models #6,1,0,0,-2.9146,0,1,0,-18.212,0,0,1,-422.7

> view matrix models #6,1,0,0,-4.8565,0,1,0,-29.155,0,0,1,-677.77

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.80391,-0.59465,0.01102,116.31,0.59459,0.80398,0.0086864,-80.079,-0.014025,-0.00043079,0.9999,-675.77

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.80391,-0.59465,0.01102,116.8,0.59459,0.80398,0.0086864,-102.32,-0.014025,-0.00043079,0.9999,-843.37

> view matrix models
> #6,0.80391,-0.59465,0.01102,112.02,0.59459,0.80398,0.0086864,-108.66,-0.014025,-0.00043079,0.9999,-896.89

> view matrix models
> #6,0.80391,-0.59465,0.01102,115.21,0.59459,0.80398,0.0086864,-77.871,-0.014025,-0.00043079,0.9999,-897.46

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.80516,-0.59177,0.038981,120.05,0.59263,0.80532,-0.01544,-82.519,-0.022256,0.035533,0.99912,-902.02

> view matrix models
> #6,0.8035,-0.59529,0.0044595,114.08,0.59526,0.80332,-0.018748,-83.221,0.0075783,0.017719,0.99981,-903.29

> view matrix models
> #6,0.59535,-0.80339,0.01154,176.55,0.8006,0.59437,0.075959,-61.109,-0.067883,-0.035983,0.99704,-885.04

> view matrix models
> #6,0.58974,-0.80727,0.02295,180.16,0.80735,0.59002,0.007616,-74.733,-0.019689,0.014037,0.99971,-898.94

> view matrix models
> #6,0.50954,-0.86044,-0.0040741,194.26,0.86014,0.50922,0.02934,-65.383,-0.023171,-0.018454,0.99956,-893.48

> view matrix models
> #6,0.50996,-0.85997,0.019719,198.78,0.86013,0.51007,0.00096818,-71.057,-0.010891,0.016467,0.99981,-900.53

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.50996,-0.85997,0.019719,200.64,0.86013,0.51007,0.00096818,-63.838,-0.010891,0.016467,0.99981,-900.43

> fitmap #6 inMap #5

Fit map volume maximum in map volume maximum using 1500382 points  
correlation = 0.2441, correlation about mean = -0.02013, overlap = 48.85  
steps = 2000, shift = 20.2, angle = 9.67 degrees  
  
Position of volume maximum (#6) relative to volume maximum (#5) coordinates:  
Matrix rotation and translation  
0.36347783 -0.93132250 -0.02285316 245.12223471  
0.93160180 0.36340491 0.00741385 -49.33659096  
0.00140027 -0.02398481 0.99971134 -893.26862208  
Axis -0.01685068 -0.01301605 0.99977329  
Axis point 159.67794754 137.84283237 0.00000000  
Rotation angle (degrees) 68.69718276  
Shift along axis -896.55441969  
  

> select subtract #6

Nothing selected  

> select add #6

2 models selected  

> select add #5

4 models selected  

> vop maximum #5 #6

Opened volume maximum as #7, grid size 860,842,2288, pixel 0.83, shown at step
1, values float32  

> volume #7 level 0.02349

> volume #7 level 0.01862

> volume #7 level 0.01695

> save D:/FUS/halfpitch_HC/donor1.cxs

ChimeraX session files cannot include maps over 4 Gbytes in size.  
  
You tried to save map "volume maximum", size 860,842,2288, type float32.
Instead save the map in a map file (e.g. *.mrc, *.cmap) then save the session
file and it will reference the map file instead of including the map data in
the session file.  
[Repeated 1 time(s)]

> close #1-4

> save D:/FUS/halfpitch_HC/donor1.cxs

Ran out of memory trying to save a session including 3 maps (9.8 Gbytes).  
  
To save the session you will either have to save the maps to separate files
(then only the path to the file is included in the session) or close some of
the maps.  
  
#5 "volume maximum" (1882 MB)  
#6 "volume maximum" (1882 MB)  
#7 "volume maximum" (6320 MB)  
[Repeated 1 time(s)]

> vop maximum #5 #6

Opened volume maximum as #1, grid size 860,842,2288, pixel 0.83, shown at step
1, values float32  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3258, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3855, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 350, in volume_maximum  
rv = combine_op(volumes, 'maximum', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 406, in combine_op  
cv = [combine_operation(volumes, operation, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 406, in <listcomp>  
cv = [combine_operation(volumes, operation, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 465, in combine_operation  
rv.combine_interpolated_values(v, op, subregion = subregion, step = step,  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1538, in combine_interpolated_values  
values, const_values = v.interpolate_on_grid(self, subregion, step)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1598, in interpolate_on_grid  
values = empty(shape, floatc)  
^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 6.17 GiB for an
array with shape (2288, 842, 860) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 6.17 GiB for an
array with shape (2288, 842, 860) and data type float32  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1598, in interpolate_on_grid  
values = empty(shape, floatc)  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> hide #!1 models

> show #!1 models

> select subtract #5

2 models selected  

> select subtract #6

Nothing selected  

> hide #!7 models

> show #!7 models

> hide #!1 models

> show #!1 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!5 models

> show #!6 models

> hide #!1 models

> vop maximum #5 #6

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3258, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3855, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 350, in volume_maximum  
rv = combine_op(volumes, 'maximum', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 406, in combine_op  
cv = [combine_operation(volumes, operation, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 406, in <listcomp>  
cv = [combine_operation(volumes, operation, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 445, in combine_operation  
rg = gv.region_grid(r, value_type = value_type, new_spacing = spacing, clamp =
False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1084, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 6.17 GiB for an
array with shape (2288, 842, 860) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 6.17 GiB for an
array with shape (2288, 842, 860) and data type float32  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1084, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open D:/FUS/map/1fl-postprocess_masked.mrc

Opened 1fl-postprocess_masked.mrc as #2, grid size 360,360,360, pixel 0.83,
shown at level 0.0195, step 2, values float32  

> hide #!2 models

> show #!2 models

> hide #!5 models

> hide #!6 models

> volume #2 step 1

> volume #2 level 0.017

> show #!7 models

> select add #7

2 models selected  

> select subtract #7

Nothing selected  

> select add #2

2 models selected  

> view matrix models #2,1,0,0,0.13582,0,1,0,-4.1492,0,0,1,187.39

> view matrix models #2,1,0,0,-1.6283,0,1,0,-3.9812,0,0,1,240.08

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.95969,0.281,-0.0061322,-40.517,-0.28102,0.9597,-0.002514,42.602,0.0051787,0.0041359,0.99998,238.69

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.95969,0.281,-0.0061322,-38.374,-0.28102,0.9597,-0.002514,44.09,0.0051787,0.0041359,0.99998,238.73

> view matrix models
> #2,0.95969,0.281,-0.0061322,-37.546,-0.28102,0.9597,-0.002514,47.395,0.0051787,0.0041359,0.99998,238.51

> fitmap #2 inMap #7

Fit map 1fl-postprocess_masked.mrc in map volume maximum using 579630 points  
correlation = 0.3083, correlation about mean = -0.1259, overlap = 35.4  
steps = 1816, shift = 4.05, angle = 1.94 degrees  
  
Position of 1fl-postprocess_masked.mrc (#2) relative to volume maximum (#7)
coordinates:  
Matrix rotation and translation  
0.94997360 0.31232123 0.00236816 -39.20468276  
-0.31230905 0.94997020 -0.00443594 54.23474088  
-0.00363512 0.00347443 0.99998736 237.48431186  
Axis 0.01266249 0.00960972 -0.99987365  
Axis point 158.33376227 141.26193920 0.00000000  
Rotation angle (degrees) 18.20118733  
Shift along axis -237.42955340  
  

> select subtract #2

Nothing selected  

> vop maximum #2 #7

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3258, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3855, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 350, in volume_maximum  
rv = combine_op(volumes, 'maximum', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 406, in combine_op  
cv = [combine_operation(volumes, operation, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 406, in <listcomp>  
cv = [combine_operation(volumes, operation, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 445, in combine_operation  
rg = gv.region_grid(r, value_type = value_type, new_spacing = spacing, clamp =
False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1084, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 11.3 GiB for an
array with shape (2576, 1079, 1091) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 11.3 GiB for an
array with shape (2576, 1079, 1091) and data type float32  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1084, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 591.55
OpenGL renderer: NVIDIA GeForce RTX 4060 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: HP
Model: Victus by HP 15L Gaming Desktop TG02-2xxx
OS: Microsoft Windows 11 家庭中文版 (Build 26200)
Memory: 16,920,178,688
MaxProcessMemory: 137,438,953,344
CPU: 28 Intel(R) Core(TM) i7-14700F
OSLanguage: zh-CN

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2026.1.4
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0