id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20229 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 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 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 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: 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