vop add: ArrayMemoryError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:/Users/syutk/Downloads/Making a map.cxs"

Opened cryosparc_P128_J691_006_volume_map (1).mrc as #1, grid size
500,500,500, pixel 0.571, shown at level 0.0264, step 2, values float32  
Opened cryosparc_P128_J691_006_volume_map (1).mrc gaussian as #2, grid size
500,500,500, pixel 0.571, shown at level 0.0117, step 1, values float32  
Opened volume_segment_CD.mrc as #4, grid size 100,100,84, pixel 0.571, shown
at level 0.0468, step 1, values float32  
Opened volume_segment_CD.mrc resampled as #5, grid size 500,500,500, pixel
0.571, shown at level 0.00926, step 1, values float32  
Opened volume sum as #6, grid size 821,702,765, pixel 0.571, shown at level
0.0117, step 1, values float32  
Opened volume sum as #7, grid size 823,769,862, pixel 0.571, shown at level
0.0117, step 1, values float32  
Opened volume sum as #8, grid size 825,773,878, pixel 0.571, shown at level
0.0117, step 1, values float32  
Opened volume sum_43_regions.mrc as #9, grid size 168,194,211, pixel 0.571,
shown at level 0.0121, step 1, values float32  
Opened mask43regions.mrc as #10, grid size 500,500,500, pixel 0.571, shown at
level 0.0121, step 1, values float32  
Opened maskSUM.mrc as #11, grid size 500,500,500, pixel 0.571, shown at level
0.0117, step 1, values float32  
Opened volume_26_regions.mrc as #12, grid size 161,171,167, pixel 0.571, shown
at level 0.0965, step 1, values float32  
Opened mask26regions.mrc as #13, grid size 500,500,500, pixel 0.571, shown at
level 0.0107, step 1, values float32  
Log from Thu Nov 21 11:52:46 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/maliona/Desktop/Cryo-EM/Factor XIa/Chimera Sessions/Making a
> map.cxs" format session

Opened cryosparc_P128_J691_006_volume_map (1).mrc as #1, grid size
500,500,500, pixel 0.571, shown at level 0.0264, step 2, values float32  
Opened cryosparc_P128_J691_006_volume_map (1).mrc gaussian as #2, grid size
500,500,500, pixel 0.571, shown at level 0.00944, step 1, values float32  
Opened volume_segment_CD.mrc as #4, grid size 100,100,84, pixel 0.571, shown
at level 0.0468, step 1, values float32  
Log from Thu Nov 21 10:58:37 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/maliona/Desktop/Cryo-EM/Factor XIa/Chimera
> Sessions/Session_w_Christos_241112.cxs" format session

Opened cryosparc_P128_J691_006_volume_map.mrc as #4, grid size 500,500,500,
pixel 0.571, shown at level 0.0209, step 2, values float32  
Opened cryosparc_P128_J693_class_00_00098_volume.mrc as #6.1, grid size
300,300,300, pixel 0.952, shown at level 0.0672, step 2, values float32  
Opened cryosparc_P128_J693_class_02_00098_volume.mrc as #6.2, grid size
300,300,300, pixel 0.952, shown at level 0.0329, step 2, values float32  
Opened cryosparc_P128_J693_class_01_00098_volume.mrc as #6.3, grid size
300,300,300, pixel 0.952, shown at level 0.0836, step 2, values float32  
Opened cryosparc_P128_J694_class_02_00099_volume.mrc as #7.1, grid size
300,300,300, pixel 0.952, shown at level 0.0196, step 2, values float32  
Opened cryosparc_P128_J694_class_01_00099_volume.mrc as #7.2, grid size
300,300,300, pixel 0.952, shown at level 0.0179, step 2, values float32  
Opened cryosparc_P128_J694_class_00_00099_volume.mrc as #7.3, grid size
300,300,300, pixel 0.952, shown at level 0.0192, step 2, values float32  
Opened cryosparc_P128_J639_003_volume_map (1).mrc as #8, grid size
112,112,112, pixel 2.55, shown at level 0.24, step 1, values float32  
Opened map 6 as #12, grid size 76,62,79, pixel 2, shown at step 1, values
float32  
Opened cryosparc_P128_J703_class_02_00098_volume.mrc as #1.1, grid size
300,300,300, pixel 0.952, shown at level 0.0331, step 2, values float32  
Opened cryosparc_P128_J703_class_01_00098_volume.mrc as #1.2, grid size
300,300,300, pixel 0.952, shown at level 0.0337, step 2, values float32  
Opened cryosparc_P128_J703_class_00_00098_volume.mrc as #1.3, grid size
300,300,300, pixel 0.952, shown at level 0.0468, step 2, values float32  
Log from Tue Nov 12 16:48:01 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/maliona/Downloads/cryosparc_P128_J683_003_volume_map.mrc

Opened cryosparc_P128_J683_003_volume_map.mrc as #1, grid size 112,112,112,
pixel 2.55, shown at level 0.0745, step 1, values float32  

> volume #1 style image

> volume #1 level -0.003579,0 level 0.07447,0.8 level 0.8808,1

> volume #1 level -0.003579,0 level 0.03439,0.7559 level 0.8808,1

> volume #1 style mesh

> volume #1 style image

> volume #1 level -0.003579,0 level 0.04714,0.6529 level 0.8808,1

> volume #1 style surface

> select add #1

3 models selected  
Drag select of 1 cryosparc_P128_J683_003_volume_map.mrc  
[Repeated 1 time(s)]

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.99348,0.10748,-0.037973,270.82,0.074058,0.86181,0.50179,-62.391,0.086659,0.49571,-0.86416,183.35

> view matrix models
> #1,-0.99416,0.10732,-0.011319,267.11,0.082679,0.82489,0.55921,-66.475,0.06935,0.55501,-0.82895,172.09

> select subtract #1

Nothing selected  

> hide #!1 models

> open /Users/maliona/Downloads/cryosparc_P128_J688_class_02_final_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J688_class_00_final_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J688_class_01_final_volume.mrc

Opened cryosparc_P128_J688_class_02_final_volume.mrc as #2.1, grid size
192,192,192, pixel 1.49, shown at level 0.0378, step 1, values float32  
Opened cryosparc_P128_J688_class_00_final_volume.mrc as #2.2, grid size
192,192,192, pixel 1.49, shown at level 0.0368, step 1, values float32  
Opened cryosparc_P128_J688_class_01_final_volume.mrc as #2.3, grid size
192,192,192, pixel 1.49, shown at level 0.0459, step 1, values float32  

> open /Users/maliona/Downloads/cryosparc_P128_J690_class_01_final_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J690_class_00_final_volume.mrc

Opened cryosparc_P128_J690_class_01_final_volume.mrc as #3.1, grid size
192,192,192, pixel 1.49, shown at level 0.0236, step 1, values float32  
Opened cryosparc_P128_J690_class_00_final_volume.mrc as #3.2, grid size
192,192,192, pixel 1.49, shown at level 0.022, step 1, values float32  

> hide #!3.2 models

> hide #!3.1 models

> hide #!3 models

> hide #!2.3 models

> hide #!2.2 models

> volume #1 level 0.2115

> hide #!1 models

> volume #2.1 level 0.1247

> volume #2.1 level 0.07053

> hide #!2.1 models

> show #!2.2 models

> volume #2.2 level 0.1034

> volume #2.2 level 0.1793

> hide #!2.2 models

> show #!2.3 models

> volume #2.3 level 0.1023

> volume #2.3 level 0.1523

> hide #!2.3 models

> show #!3.1 models

> volume #3.1 level 0.1029

> volume #3.1 level 0.06669

> volume #3.1 level 0.08651

> hide #!3.1 models

> show #!3.2 models

> volume #3.2 level 0.08448

> hide #!3 models

> hide #!3.2 models

> show #!2.2 models

> volume #2.2 level 0.1244

> show #!2.3 models

> hide #!2.2 models

> open /Users/maliona/Downloads/cryosparc_P128_J691_006_volume_map.mrc

Opened cryosparc_P128_J691_006_volume_map.mrc as #4, grid size 500,500,500,
pixel 0.571, shown at level 0.00726, step 2, values float32  

> hide #!2 models

> volume #4 level 0.02419

> ui tool show "Selection Inspector"

> volume #4 level 0.0788

> volume #4 level 0.07115

> volume #4 level 0.01327

> volume #4 level 0.04112

> volume #4 level 0.01272

> volume #4 level 0.04767

> hide #!2.3 models

> hide #!4 models

> open /Users/maliona/Downloads/cryosparc_P128_J692_class_00_00098_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J692_class_02_00098_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J692_class_01_00098_volume.mrc

Opened cryosparc_P128_J692_class_00_00098_volume.mrc as #5.1, grid size
300,300,300, pixel 0.952, shown at level 0.0194, step 2, values float32  
Opened cryosparc_P128_J692_class_02_00098_volume.mrc as #5.2, grid size
300,300,300, pixel 0.952, shown at level 0.0192, step 2, values float32  
Opened cryosparc_P128_J692_class_01_00098_volume.mrc as #5.3, grid size
300,300,300, pixel 0.952, shown at level 0.0175, step 2, values float32  

> open /Users/maliona/Downloads/cryosparc_P128_J693_class_00_00098_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J693_class_02_00098_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J693_class_01_00098_volume.mrc

Opened cryosparc_P128_J693_class_00_00098_volume.mrc as #6.1, grid size
300,300,300, pixel 0.952, shown at level 0.019, step 2, values float32  
Opened cryosparc_P128_J693_class_02_00098_volume.mrc as #6.2, grid size
300,300,300, pixel 0.952, shown at level 0.0186, step 2, values float32  
Opened cryosparc_P128_J693_class_01_00098_volume.mrc as #6.3, grid size
300,300,300, pixel 0.952, shown at level 0.0202, step 2, values float32  

> open /Users/maliona/Downloads/cryosparc_P128_J694_class_02_00099_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J694_class_01_00099_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J694_class_00_00099_volume.mrc

Opened cryosparc_P128_J694_class_02_00099_volume.mrc as #7.1, grid size
300,300,300, pixel 0.952, shown at level 0.0196, step 2, values float32  
Opened cryosparc_P128_J694_class_01_00099_volume.mrc as #7.2, grid size
300,300,300, pixel 0.952, shown at level 0.0179, step 2, values float32  
Opened cryosparc_P128_J694_class_00_00099_volume.mrc as #7.3, grid size
300,300,300, pixel 0.952, shown at level 0.0192, step 2, values float32  

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> hide #!5.3 models

> hide #!5.2 models

> volume #5.1 level 0.049

> volume #5.1 level 0.08016

> hide #!5.1 models

> show #!5.2 models

> volume #5.2 level 0.06893

> hide #!5.2 models

> show #!5.3 models

> volume #5.3 level 0.08765

> hide #!5.3 models

> show #!5.2 models

> hide #!5.2 models

> show #!6 models

> hide #!6.3 models

> hide #!6.2 models

> volume #6.1 level 0.0672

> hide #!6.1 models

> show #!6.3 models

> volume #6.3 level 0.06149

> volume #6.3 level 0.08355

> hide #!6.3 models

> show #!2.1 models

> show #!2.2 models

> show #!2.3 models

> hide #!2.3 models

> hide #!2.2 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.3 models

> volume #2.3 level 0.07413

> open "/Users/maliona/Downloads/cryosparc_P128_J639_003_volume_map (1).mrc"

Opened cryosparc_P128_J639_003_volume_map (1).mrc as #8, grid size
112,112,112, pixel 2.55, shown at level 0.126, step 1, values float32  

> hide #!2.3 models

> hide #!2 models

> volume #8 level 0.2282

> volume #8 level 0.2402

> open 6i58

6i58 title:  
Allosteric activation of human prekallikrein by apple domain disc rotation
[more info...]  
  
Chain information for 6i58 #9  
---  
Chain | Description | UniProt  
A | Coagulation factor XI | FA11_HUMAN 1-607  
  
Non-standard residues in 6i58 #9  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PEG — di(hydroxyethyl)ether  
  
6i58 mmCIF Assemblies  
---  
1| software_defined_assembly  
  

> hide #!8 models

> hide #!7.3 models

> hide #!7.2 models

> hide #!7.1 models

> hide #!5 models

> hide #!6 models

> show #!8 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> sym #9 assembly 1

Made 2 copies for 6i58 assembly 1  

> view

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> select add #10

9500 atoms, 9576 bonds, 8 pseudobonds, 1356 residues, 5 models selected  

> ui mousemode right "translate selected models"

> view matrix models #10,1,0,0,202.89,0,1,0,58.997,0,0,1,118.58

> view matrix models #10,1,0,0,162.51,0,1,0,63.798,0,0,1,129.13

> select subtract #10

Nothing selected  

> hide #!2.2 models

> hide #!2 models

> show #!2.3 models

> volume #2.2 level 0.1454

> volume #2.3 level 0.2184

> volume #2.3 level 0.07196

> vop flip #2.3

Opened cryosparc_P128_J688_class_01_final_volume.mrc z flip as #11, grid size
192,192,192, pixel 1.49, shown at step 1, values float32  

> hide #!2 models

> fitmap #10 inMap #11

Fit molecules 6i58 (#10.1), 6i58 (#10.2) to map
cryosparc_P128_J688_class_01_final_volume.mrc z flip (#11) using 9500 atoms  
average map value = 0.06591, steps = 196  
shifted from previous position = 19.9  
rotated from previous position = 33 degrees  
atoms outside contour = 6322, contour level = 0.071963  
  
Position of 6i58 (#10.1) relative to
cryosparc_P128_J688_class_01_final_volume.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.87203037 0.44460128 -0.20467713 -15.08375380  
-0.37435673 0.87524742 0.30626621 10.05841365  
0.31530948 -0.19045118 0.92968182 12.31495130  
Axis -0.45576033 -0.47711088 -0.75143046  
Axis point 3.61524819 42.32544910 0.00000000  
Rotation angle (degrees) 33.02006246  
Shift along axis -7.17823147  
  
Position of 6i58 (#10.2) relative to
cryosparc_P128_J688_class_01_final_volume.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.44460128 0.87203037 0.20467713 -49.60292740  
0.87524742 -0.37435673 -0.30626621 110.97644484  
-0.19045118 0.31530948 -0.92968182 -28.53027896  
Axis 0.84391154 0.53646457 0.00436778  
Axis point 0.00000000 74.48879617 -2.65324021  
Rotation angle (degrees) 158.39099738  
Shift along axis 17.54983452  
  

> select add #10

9500 atoms, 9576 bonds, 8 pseudobonds, 1356 residues, 5 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.63948,-0.59698,-0.48444,194.16,0.74777,0.62938,0.21149,101.25,0.17864,-0.49749,0.84888,164.19

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.63948,-0.59698,-0.48444,197.92,0.74777,0.62938,0.21149,111.36,0.17864,-0.49749,0.84888,185.88

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.33494,-0.61446,-0.71432,192.91,0.9215,0.055418,0.38441,153.75,-0.19662,-0.787,0.58478,197.87

> view matrix models
> #10,0.29487,-0.64411,-0.70581,194.34,0.95452,0.23256,0.18655,141.07,0.043984,-0.72872,0.68339,198.2

> view matrix models
> #10,0.20104,-0.70486,-0.68026,197.16,0.97943,0.1571,0.12667,146.12,0.017582,-0.69173,0.72194,195.57

> fitmap #10 inMap #11

Fit molecules 6i58 (#10.1), 6i58 (#10.2) to map
cryosparc_P128_J688_class_01_final_volume.mrc z flip (#11) using 9500 atoms  
average map value = 0.08667, steps = 156  
shifted from previous position = 9.65  
rotated from previous position = 32 degrees  
atoms outside contour = 5080, contour level = 0.071963  
  
Position of 6i58 (#10.1) relative to
cryosparc_P128_J688_class_01_final_volume.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.79130913 0.11371712 -0.60074810 5.85545877  
-0.14543558 0.98935842 -0.00429050 13.20995689  
0.59386729 0.09076527 0.79942687 13.05387780  
Axis 0.07752743 -0.97432767 -0.21136481  
Axis point -11.30055875 0.00000000 15.63107473  
Rotation angle (degrees) 37.81007676  
Shift along axis -15.17599825  
  
Position of 6i58 (#10.2) relative to
cryosparc_P128_J688_class_01_final_volume.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.11371712 0.79130913 0.60074810 -48.86687162  
0.98935842 -0.14543558 0.00429050 104.85592058  
0.09076527 0.59386729 -0.79942687 -27.57664146  
Axis 0.73302623 0.63406634 0.24623650  
Axis point 0.00000000 78.35365076 7.26689512  
Rotation angle (degrees) 156.28718410  
Shift along axis 23.87453569  
  

> volume #11 level 0.1761

> volume #11 level 0.09692

> volume #11 level 0.1132

> volume #11 level 0.08607

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.20104,-0.70486,-0.68026,272.31,0.97943,0.1571,0.12667,160.76,0.017582,-0.69173,0.72194,202

> select subtract #10

Nothing selected  

> volume #11 style image

> volume #11 style surface

> molmap #10 6

Opened map 6 as #12, grid size 76,62,79, pixel 2, shown at level 0.0973, step
1, values float32  

> fitmap #12 inMap #11

Fit map map 6 in map cryosparc_P128_J688_class_01_final_volume.mrc z flip
using 23278 points  
correlation = 0.7222, correlation about mean = 0.1012, overlap = 655.7  
steps = 332, shift = 75.9, angle = 2.4 degrees  
  
Position of map 6 (#12) relative to
cryosparc_P128_J688_class_01_final_volume.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.81071105 0.08425357 -0.57935216 -67.21680159  
-0.11556883 0.99314899 -0.01728927 -8.87330080  
0.57392634 0.08097166 0.81489395 13.26994204  
Axis 0.08365631 -0.98186553 -0.17012260  
Axis point -55.02760419 0.00000000 -98.16182598  
Rotation angle (degrees) 35.96489299  
Shift along axis 0.83176159  
  

> select add #12

2 models selected  

> view matrix models
> #12,0.81071,0.084254,-0.57935,-122.86,-0.11557,0.99315,-0.017289,9.6632,0.57393,0.080972,0.81489,20.537

> view matrix models
> #12,0.81071,0.084254,-0.57935,-50.349,-0.11557,0.99315,-0.017289,73.498,0.57393,0.080972,0.81489,-4.9246

> view matrix models
> #12,0.81071,0.084254,-0.57935,-26.168,-0.11557,0.99315,-0.017289,77.15,0.57393,0.080972,0.81489,-11.386

> select up

4750 atoms, 4788 bonds, 678 residues, 17 models selected  

> select add #11

4750 atoms, 4788 bonds, 678 residues, 18 models selected  

> select add #11

4750 atoms, 4788 bonds, 678 residues, 18 models selected  

> hide #!11 models

> select add #11

4750 atoms, 4788 bonds, 678 residues, 18 models selected  

> select add #11

4750 atoms, 4788 bonds, 678 residues, 18 models selected  

> select add #10

14250 atoms, 14364 bonds, 8 pseudobonds, 2034 residues, 22 models selected  

> select add #9

14250 atoms, 14364 bonds, 12 pseudobonds, 2034 residues, 23 models selected  

> select subtract #9

9500 atoms, 9576 bonds, 8 pseudobonds, 1356 residues, 21 models selected  

> select subtract #10

16 models selected  

> select add #10.1

4750 atoms, 4788 bonds, 4 pseudobonds, 678 residues, 18 models selected  

> select add #11

4750 atoms, 4788 bonds, 4 pseudobonds, 678 residues, 18 models selected  

> view matrix models
> #1,-0.99416,0.10732,-0.011319,267.08,0.082679,0.82489,0.55921,-66.472,0.06935,0.55501,-0.82895,172.22,#2,1,0,0,-0.036313,0,1,0,0.0031097,0,0,1,0.12894,#3,1,0,0,-0.036313,0,1,0,0.0031097,0,0,1,0.12894,#4,1,0,0,-0.036313,0,1,0,0.0031097,0,0,1,0.12894,#5,1,0,0,-0.036313,0,1,0,0.0031097,0,0,1,0.12894,#6,1,0,0,-0.036313,0,1,0,0.0031097,0,0,1,0.12894,#7,1,0,0,-0.036313,0,1,0,0.0031097,0,0,1,0.12894,#8,1,0,0,-0.036313,0,1,0,0.0031097,0,0,1,0.12894,#10.1,0.79131,0.11372,-0.60075,5.8535,-0.14544,0.98936,-0.0042905,13.147,0.59387,0.090765,0.79943,13.172,#11,1,0,0,-0.036313,0,1,0,0.0031097,0,0,1,0.12894,#12,0.81071,0.084254,-0.57935,-26.205,-0.11557,0.99315,-0.017289,77.153,0.57393,0.080972,0.81489,-11.257

> select #12

2 models selected  

> select #12

2 models selected  

> select #12

2 models selected  

> select #12

2 models selected  

> select subtract #12

Nothing selected  

> show #!2.3 models

> select add #2.3

2 models selected  

> view matrix models #2.3,1,0,0,66.926,0,1,0,56.01,0,0,1,-7.5187

> view matrix models #2.3,1,0,0,58.521,0,1,0,91.616,0,0,1,-12.32

> select down

2 models selected  

> hide #9.1 models

> hide #!10 models

> hide #!10.1 models

> hide #!10.2 models

> fitmap #12 inMap #2.3

Fit map map 6 in map cryosparc_P128_J688_class_01_final_volume.mrc using 23278
points  
correlation = 0.8315, correlation about mean = 0.3589, overlap = 858.6  
steps = 180, shift = 12.9, angle = 41.5 degrees  
  
Position of map 6 (#12) relative to
cryosparc_P128_J688_class_01_final_volume.mrc (#2.3) coordinates:  
Matrix rotation and translation  
0.46028308 0.60277351 -0.65176957 -85.85572845  
-0.72377370 0.67992826 0.11768263 186.28860753  
0.51409252 0.41756635 0.74923109 -48.14817737  
Axis 0.16740766 -0.65083308 -0.74053425  
Axis point 83.66073157 189.58151739 0.00000000  
Rotation angle (degrees) 63.59449660  
Shift along axis -99.96032103  
  

> volume #12 style image

> volume #12 level 0,0 level 0.489,0.8 level 0.7419,1

> volume #12 level 0,0 level 0.0131,0.7538 level 0.7419,1

> select subtract #2.3

Nothing selected  

> volume #2.3 style image

> volume #2.3 level -7.273e-05,0 level 0.04589,0.8 level 0.541,1

> volume #2.3 level -7.273e-05,0 level 0.03396,0.8294 level 0.541,1

> volume #2.3 level -7.273e-05,0 level 0.01551,0.6088 level 0.541,1

> volume #2.3 level -7.273e-05,0 level 0.07519,0.7265 level 0.541,1

> volume #2.3 color #b3b3ff color #fffc79 color #b3b3ff

> volume #2.3 color #b3b3ff color #ff2600 color #b3b3ff

> hide #!2.3 models

> show #!2.3 models

> hide #!12 models

> volume #2.3 level -7.273e-05,0 level 0.01877,0.5588 level 0.541,1

> set bgColor white

> set bgColor #ffffff00

> volume #2.3 level -7.273e-05,0 level 0.2097,1 level 0.541,1

> volume #2.3 color #b3b3ff color #ffd479 color #b3b3ff

> volume #2.3

> volume #2.3 style surface

> volume #2.3 style image

> show #!4 models

> volume #4 style image

> volume #4 level -0.00106,0 level 0.007243,0.8 level 0.2105,1

> volume #4 level -0.00106,0 level 0.01216,0.3882 level 0.2105,1

> set bgColor black

> set bgColor transparent

> set bgColor black

> set bgColor white

> set bgColor #ffffff00

> show #!12 models

> select add #12

3 models selected  

> view matrix models
> #12,0.46028,0.60277,-0.65177,-97.792,-0.72377,0.67993,0.11768,195.51,0.51409,0.41757,0.74923,-39.109

> view matrix models
> #12,0.46028,0.60277,-0.65177,-96.142,-0.72377,0.67993,0.11768,200.85,0.51409,0.41757,0.74923,-44.849

> fitmap #12 inMap #4

Fit map map 6 in map cryosparc_P128_J691_006_volume_map.mrc using 23278 points  
correlation = 0.6989, correlation about mean = 0.4094, overlap = 230.2  
steps = 212, shift = 17.9, angle = 0.594 degrees  
  
Position of map 6 (#12) relative to cryosparc_P128_J691_006_volume_map.mrc
(#4) coordinates:  
Matrix rotation and translation  
0.46137870 0.60939007 -0.64480496 -87.29058049  
-0.72393733 0.67873005 0.12345142 186.91639616  
0.51287857 0.40984053 0.75431182 -46.63474200  
Axis 0.16009608 -0.64716357 -0.74535130  
Axis point 83.85655266 191.04168228 0.00000000  
Rotation angle (degrees) 63.43516079  
Shift along axis -100.18109627  
  

> set bgColor black

> set bgColor transparent

> volume #4 level -0.00106,0 level 0.01653,0.9324 level 0.2105,1

> volume #12 level 0,0 level 0.04328,0.3692 level 0.7419,1

> volume #12 style surface

> volume #4 style surface

> volume #4 level 0.003435

> volume #4 level 0.008896

> volume #4 level 0.01381

> volume #4 level 0.01436

> select add #12

3 models selected  

> select add #12

3 models selected  

> volume #12 style image

> volume #12 level 0,0 level 0,0.6923 level 0.7419,1

> volume #4 level 0.01163

> open /Users/maliona/Downloads/3h9v.pdb

3h9v.pdb title:  
Crystal structure of the atp-gated P2X4 ion channel In the closed, apo state
At 3.1 angstroms [more info...]  
  
Chain information for 3h9v.pdb #13  
---  
Chain | Description | UniProt  
A | P2X purinoceptor | Q6NYR1_DANRE 28-381  
  
Non-standard residues in 3h9v.pdb #13  
---  
GD — gadolinium atom  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  

> hide #!12 models

> hide #!4 models

> select #13/A:32-361

2443 atoms, 2503 bonds, 1 pseudobond, 329 residues, 2 models selected  

> sequence chain #13/A

Alignment identifier is 13/A  

> close #13

> open 3h9v

Summary of feedback from opening 3h9v fetched from pdb  
---  
notes | Fetching compressed mmCIF 3h9v from http://files.rcsb.org/download/3h9v.cif  
Fetching CCD GD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/GD/GD.cif  
  
3h9v title:  
Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state
at 3.1 Angstroms [more info...]  
  
Chain information for 3h9v #13  
---  
Chain | Description | UniProt  
A | P2X purinoceptor | Q6NYR1_DANRE 28-381  
  
Non-standard residues in 3h9v #13  
---  
GD — gadolinium atom  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3h9v mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> sym #13 assembly 1

Made 3 copies for 3h9v assembly 1  

> view

> color #14.1 #73fcd6ff

> color #14.2 #fffb00ff

> color #14.2 #fffc79ff

> color #14.3 #ff7e79ff

> set bgColor white

> set bgColor #ffffff00

> select add #14

7503 atoms, 7689 bonds, 3 pseudobonds, 1005 residues, 7 models selected  

> select ligand

413 atoms, 421 bonds, 31 residues, 7 models selected  

> select add #9

5100 atoms, 5146 bonds, 4 pseudobonds, 704 residues, 8 models selected  

> select subtract #9

350 atoms, 358 bonds, 26 residues, 6 models selected  

> select add #10

9724 atoms, 9808 bonds, 8 pseudobonds, 1372 residues, 9 models selected  

> select subtract #10

224 atoms, 232 bonds, 16 residues, 4 models selected  

> hide #!2 models

> select add #13

2669 atoms, 2737 bonds, 1 pseudobond, 347 residues, 5 models selected  

> select subtract #13

168 atoms, 174 bonds, 12 residues, 3 models selected  

> delete atoms sel

> delete bonds sel

> select solvent

249 atoms, 249 residues, 3 models selected  

> select ions

23 atoms, 23 residues, 7 models selected  

> select add #9

4768 atoms, 4788 bonds, 4 pseudobonds, 696 residues, 8 models selected  

> select subtract #9

18 atoms, 18 residues, 6 models selected  

> select add #10

9508 atoms, 9576 bonds, 8 pseudobonds, 1364 residues, 9 models selected  

> select subtract #10

8 atoms, 8 residues, 4 models selected  

> select add #13

2507 atoms, 2563 bonds, 1 pseudobond, 341 residues, 5 models selected  

> select subtract #13

6 atoms, 6 residues, 3 models selected  

> delete atoms sel

> delete bonds sel

> save /Users/maliona/Desktop/image1.png supersample 3

> show #!4 models

> close #13-14

> set bgColor black

> set bgColor transparent

> select add #4

3 models selected  

> view matrix models
> #4,0.95346,0.30074,-0.021814,-32.439,-0.30153,0.95042,-0.075998,60.462,-0.0021234,0.079038,0.99687,-10.189

> show #!12 models

> hide #!12 models

> select add #4

3 models selected  

> select add #4

3 models selected  

> volume #4 level 0.04549

> volume #4 level 0.0504

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4

3 models selected  

> select add #4.2

3 models selected  

> select subtract #4.1

2 models selected  

> set bgColor white

> set bgColor #ffffff00

> save /Users/maliona/Desktop/image2.png supersample 3

> set bgColor black

> set bgColor transparent

> close #1

> close #2

> close #3

> close #5

> close #11

> open /Users/maliona/Downloads/cryosparc_P128_J703_class_02_00098_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J703_class_01_00098_volume.mrc
> /Users/maliona/Downloads/cryosparc_P128_J703_class_00_00098_volume.mrc

Opened cryosparc_P128_J703_class_02_00098_volume.mrc as #1.1, grid size
300,300,300, pixel 0.952, shown at level 0.0193, step 2, values float32  
Opened cryosparc_P128_J703_class_01_00098_volume.mrc as #1.2, grid size
300,300,300, pixel 0.952, shown at level 0.0187, step 2, values float32  
Opened cryosparc_P128_J703_class_00_00098_volume.mrc as #1.3, grid size
300,300,300, pixel 0.952, shown at level 0.0191, step 2, values float32  

> hide #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> show #!1.1 models

> volume #1.2 level 0.04707

> volume #1.2 level 0.03366

> volume #1.3 level 0.04679

> volume #1.1 level 0.03306

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> hide #4.1 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.1 models

> hide #!1.1 models

> show #4.1 models

> volume #4 level 0.07334

> show #!12 models

> volume #12 level 0,0.01538 level 0,0.6923 level 0.7419,1

> volume #4 level 0.02637

> volume #4 level 0.01654

> volume #4 level 0.01053

> volume #6.2 level 0.03294

> volume #4 level 0.02146

> volume #4 level 0.02419

> volume #4 level 0.02036

> hide #!12 models

> volume #4 level 0.0646

> volume #4 level 0.0149

> volume #4 level 0.03019

> view matrix models
> #4,0.95346,0.30074,-0.021814,-31.183,-0.30153,0.95042,-0.075998,59.578,-0.0021234,0.079038,0.99687,-13.859

> view matrix models
> #4,0.95346,0.30074,-0.021814,-31.246,-0.30153,0.95042,-0.075998,58.53,-0.0021234,0.079038,0.99687,-13.04

> view matrix models
> #4,0.95346,0.30074,-0.021814,-32.231,-0.30153,0.95042,-0.075998,70.299,-0.0021234,0.079038,0.99687,-16.601

> volume #4 level 0.02091

> save "/Users/maliona/Desktop/Cryo-EM/Factor XIa/Chimera
> Sessions/Session_w_Christos_241112.cxs" includeMaps true

——— End of log from Tue Nov 12 16:48:01 2024 ———

opened ChimeraX session  

> close session

> open /Users/maliona/Downloads/cryosparc_P128_J691_006_volume_map.mrc

Opened cryosparc_P128_J691_006_volume_map.mrc as #1, grid size 500,500,500,
pixel 0.571, shown at level 0.00726, step 2, values float32  

> close

> open "/Users/maliona/Downloads/cryosparc_P128_J691_006_volume_map (1).mrc"

Opened cryosparc_P128_J691_006_volume_map (1).mrc as #1, grid size
500,500,500, pixel 0.571, shown at level 0.00726, step 2, values float32  

> volume #1 level 0.01521

> volume #1 level 0.02635

> volume gaussian #1 sDev 2

Opened cryosparc_P128_J691_006_volume_map (1).mrc gaussian as #2, grid size
500,500,500, pixel 0.571, shown at step 1, values float32  

> ui tool show "Segment Map"

> select add #2

2 models selected  
Segmenting cryosparc_P128_J691_006_volume_map (1).mrc gaussian, density
threshold 0.009444  
Showing 50 region surfaces  
222 watershed regions, grouped to 50 regions  
Showing cryosparc_P128_J691_006_volume_map (1) gaussian.seg - 50 regions, 50
surfaces  

> select subtract #2

Nothing selected  

> select #3.32

1 model selected  

> select #3.39

1 model selected  

> select #3.10

1 model selected  

> select #3.32

1 model selected  

> select #3.39

1 model selected  

> select add #3.40

2 models selected  

> select add #3.41

3 models selected  

> select add #3.42

4 models selected  

> select add #3.50

5 models selected  

> select subtract #3.50

4 models selected  

> select add #3.49

5 models selected  

> select add #3.48

6 models selected  

> select subtract #3.48

5 models selected  

> select add #3.47

6 models selected  

> select subtract #3.47

5 models selected  

> select add #3.46

6 models selected  

> select subtract #3.46

5 models selected  

> select subtract #3.49

4 models selected  

> select subtract #3.42

3 models selected  

> select subtract #3.41

2 models selected  

> select subtract #3.40

1 model selected  

> select subtract #3.39

Nothing selected  

> select #3.10

1 model selected  

> select #3.44

1 model selected  

> select #3.21

1 model selected  

> select add #3.10

2 models selected  

> select add #3.44

3 models selected  

> select add #3.39

4 models selected  

> select add #3.32

5 models selected  

> select add #3.24

6 models selected  
Drag select of 300, 7076 of 67080 triangles, 332, 2631 of 39024 triangles,
333, 2545 of 32696 triangles, 344, 1099 of 22312 triangles, 2
cryosparc_P128_J691_006_volume_map (1).mrc gaussian  

> select add #3.49

11 models selected  

> select add #3.29

12 models selected  

> select add #3.23

13 models selected  

> select add #3.24

14 models selected  

> select subtract #2

12 models selected  

> hide #!2 models

> hide #3.1 models

> show #3.1 models

Grouped 12 regions  
0 or more than 1 volume model selected  

> select #3.1

1 model selected  
Deleted 38 regions  

> hide #3.1 models

> hide #!3 models

> show #!2 models

> show #3.1 models

> select add #3.1

1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3.1,1,0,0,21.126,0,1,0,29.818,0,0,1,-85.148

> view matrix models #3.1,1,0,0,20.242,0,1,0,68.151,0,0,1,-50.534

> view matrix models #3.1,1,0,0,17.5,0,1,0,76.048,0,0,1,-8.8366

> view matrix models #3.1,1,0,0,30.086,0,1,0,57.883,0,0,1,-53.695

> ui mousemode right "rotate selected models"

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,138.64,0.65295,0.37318,0.65908,-55.828,0.72937,-0.54434,-0.41438,187

> ui mousemode right "translate selected models"

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,133.2,0.65295,0.37318,0.65908,-99.57,0.72937,-0.54434,-0.41438,152.1

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,117.42,0.65295,0.37318,0.65908,-95.807,0.72937,-0.54434,-0.41438,152.3

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,115.17,0.65295,0.37318,0.65908,-86.805,0.72937,-0.54434,-0.41438,151.6

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,114.32,0.65295,0.37318,0.65908,-90.202,0.72937,-0.54434,-0.41438,153.7

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,112.46,0.65295,0.37318,0.65908,-79.507,0.72937,-0.54434,-0.41438,156.19

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,109.54,0.65295,0.37318,0.65908,-59.644,0.72937,-0.54434,-0.41438,146.98

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,116.73,0.65295,0.37318,0.65908,-86.952,0.72937,-0.54434,-0.41438,154.69

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,117.51,0.65295,0.37318,0.65908,-85.55,0.72937,-0.54434,-0.41438,153.03

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,118.42,0.65295,0.37318,0.65908,-87.664,0.72937,-0.54434,-0.41438,154.68

> volume #2 style image

> volume #2 level -0.0003079,0 level 0.009441,0.8 level 0.06477,1

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,120.73,0.65295,0.37318,0.65908,-90.849,0.72937,-0.54434,-0.41438,153.66

> select subtract #3.1

Nothing selected  

> volume #2 style mesh

> volume #2 color #8efa00

> select add #3.1

1 model selected  

> view matrix models
> #3.1,0.20413,0.75129,-0.62762,118.73,0.65295,0.37318,0.65908,-92.656,0.72937,-0.54434,-0.41438,155.14

> vop add #2 #3.1

Opened cryosparc_P128_J691_006_volume_map (1).mrc gaussian resampled as #4,
grid size 500,500,500, pixel 0.571, shown at step 1, values float32  

> hide #3.1 models

> show #3.1 models

> molmap #3.1

Missing or invalid "resolution" argument: Expected a number  

> molmap #3.1 6

No atoms specified  

> close #4

> volume resample #3.1 onGrid #2

> vop add #2 #3.1

Opened cryosparc_P128_J691_006_volume_map (1).mrc gaussian resampled as #4,
grid size 500,500,500, pixel 0.571, shown at step 1, values float32  

> hide #3.1 models

> show #3.1 models

> volume resample #3.1 onGrid #1

> hide #3.1 models

> show #3.1 models

> close #4

> vop add #2 #3

Opened cryosparc_P128_J691_006_volume_map (1).mrc gaussian resampled as #4,
grid size 500,500,500, pixel 0.571, shown at step 1, values float32  

> hide #3.1 models

> show #3.1 models

> close #4

> volume resample #3 onGrid #1

> ui tool show "Segment Map"

Saving 1 regions to mrc file...  
Opened volume_segment_CD.mrc as #4, grid size 100,100,84, pixel 0.571, shown
at step 1, values float32  
Wrote volume_segment_CD.mrc  

> save "/Users/maliona/Desktop/Cryo-EM/Factor XIa/Chimera Sessions/Making a
> map.cxs" includeMaps true

——— End of log from Thu Nov 21 10:58:37 2024 ———

opened ChimeraX session  
Showing cryosparc_P128_J691_006_volume_map (1) gaussian.seg - 1 regions, 1
surfaces  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> volume resample #4 onGrid #2

Opened volume_segment_CD.mrc resampled as #5, grid size 500,500,500, pixel
0.571, shown at step 1, values float32  

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> hide #!3 models

> hide #3.1 models

> hide #!5 models

> show #!5 models

> volume #5 level 0.01018

> show #!2 models

> hide #!5 models

> show #!5 models

> volume #5 level 0.009259

> volume #2 level 0.01167

> select add #5

2 models selected  

> show #3.1 models

> hide #3.1 models

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,1.9105,0,1,0,3.0622,0,0,1,-79.241

> view matrix models #5,1,0,0,-1.8094,0,1,0,13.413,0,0,1,-82.816

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.58105,-0.20796,0.78685,-57.293,-0.81363,-0.12475,0.56785,188.17,-0.019928,-0.97015,-0.24168,290.87

> view matrix models
> #5,0.15558,-0.2221,0.96253,-29.883,-0.93443,0.28291,0.21632,207.21,-0.32035,-0.93308,-0.16352,311.51

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.15558,-0.2221,0.96253,-21.623,-0.93443,0.28291,0.21632,199.63,-0.32035,-0.93308,-0.16352,302.79

> view matrix models
> #5,0.15558,-0.2221,0.96253,-23.274,-0.93443,0.28291,0.21632,200.01,-0.32035,-0.93308,-0.16352,301.27

> view matrix models
> #5,0.15558,-0.2221,0.96253,-73.713,-0.93443,0.28291,0.21632,178.96,-0.32035,-0.93308,-0.16352,275.77

> view matrix models
> #5,0.15558,-0.2221,0.96253,-73.596,-0.93443,0.28291,0.21632,172.73,-0.32035,-0.93308,-0.16352,269.61

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.25401,-0.94138,-0.22199,236.19,-0.91016,-0.15499,-0.38417,344.2,0.32724,0.29963,-0.89618,130.94

> view matrix models
> #5,0.11767,-0.90483,-0.40919,283.06,-0.99093,-0.1339,0.011117,280.08,-0.064849,0.40417,-0.91238,170.95

> view matrix models
> #5,0.069697,-0.9956,-0.062658,240.15,-0.97425,-0.081435,0.21027,233.78,-0.21444,0.04639,-0.97563,256.17

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.069697,-0.9956,-0.062658,246.61,-0.97425,-0.081435,0.21027,241,-0.21444,0.04639,-0.97563,303.74

> view matrix models
> #5,0.069697,-0.9956,-0.062658,292.73,-0.97425,-0.081435,0.21027,273.56,-0.21444,0.04639,-0.97563,292.78

> view matrix models
> #5,0.069697,-0.9956,-0.062658,290.17,-0.97425,-0.081435,0.21027,270.45,-0.21444,0.04639,-0.97563,294.56

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.77239,0.27876,-0.57071,304.77,-0.07125,0.85484,0.51397,-46.463,0.63115,0.43765,-0.64041,61.307

> view matrix models
> #5,-0.68426,0.15502,-0.71257,337.24,0.0073088,0.97855,0.20587,-19.578,0.7292,0.13566,-0.67072,98.881

> view matrix models
> #5,0.2591,-0.64563,-0.71835,331.41,0.1507,0.76167,-0.6302,145.56,0.95402,0.055027,0.29464,-94.688

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.2591,-0.64563,-0.71835,333.59,0.1507,0.76167,-0.6302,125.76,0.95402,0.055027,0.29464,-143.52

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.76912,0.30979,-0.559,299.73,0.16561,0.9414,0.29384,-71.092,0.61727,0.13342,-0.77535,84.451

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.76912,0.30979,-0.559,301.41,0.16561,0.9414,0.29384,-70.224,0.61727,0.13342,-0.77535,135.17

> view matrix models
> #5,-0.76912,0.30979,-0.559,299.74,0.16561,0.9414,0.29384,-57.683,0.61727,0.13342,-0.77535,128.63

> view matrix models
> #5,-0.76912,0.30979,-0.559,304.02,0.16561,0.9414,0.29384,-49.035,0.61727,0.13342,-0.77535,126

> view matrix models
> #5,-0.76912,0.30979,-0.559,303.02,0.16561,0.9414,0.29384,-47.862,0.61727,0.13342,-0.77535,122.4

> vop add #2 #5

Opened volume sum as #6, grid size 821,702,765, pixel 0.571, shown at step 1,
values float32  

> select subtract #5

Nothing selected  

> show #!5 models

> select add #5

2 models selected  

> hide #!2 models

> hide #!3 models

> view matrix models
> #5,-0.76912,0.30979,-0.559,312.75,0.16561,0.9414,0.29384,-50.034,0.61727,0.13342,-0.77535,131.96

> view matrix models
> #5,-0.76912,0.30979,-0.559,316.49,0.16561,0.9414,0.29384,-51.164,0.61727,0.13342,-0.77535,131.1

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.7783,0.54573,-0.31054,237.22,0.096355,0.59251,0.79978,-81.508,0.62046,0.59254,-0.51373,14.336

> view matrix models
> #5,-0.75082,0.57036,-0.3331,233.93,0.062467,0.56337,0.82384,-76.956,0.65755,0.59775,-0.45862,-1.4474

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.75082,0.57036,-0.3331,247.89,0.062467,0.56337,0.82384,-74.625,0.65755,0.59775,-0.45862,-9.7643

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.77658,0.61521,-0.13583,208.79,0.20398,0.4495,0.86968,-84.922,0.59609,0.64766,-0.47457,-6.0809

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.77658,0.61521,-0.13583,202.58,0.20398,0.4495,0.86968,-84.888,0.59609,0.64766,-0.47457,0.54185

> view matrix models
> #5,-0.77658,0.61521,-0.13583,201.36,0.20398,0.4495,0.86968,-85.238,0.59609,0.64766,-0.47457,2.0494

> vop add #6 #5

Opened volume sum as #7, grid size 823,769,862, pixel 0.571, shown at step 1,
values float32  

> show #!5 models

> view matrix models
> #5,-0.77658,0.61521,-0.13583,195.35,0.20398,0.4495,0.86968,-86.541,0.59609,0.64766,-0.47457,-3.379

> view matrix models
> #5,-0.77658,0.61521,-0.13583,194.4,0.20398,0.4495,0.86968,-81.495,0.59609,0.64766,-0.47457,-5.7618

> view matrix models
> #5,-0.77658,0.61521,-0.13583,192.15,0.20398,0.4495,0.86968,-81.326,0.59609,0.64766,-0.47457,-4.4964

> view matrix models
> #5,-0.77658,0.61521,-0.13583,192.4,0.20398,0.4495,0.86968,-78.073,0.59609,0.64766,-0.47457,-5.9698

> view matrix models
> #5,-0.77658,0.61521,-0.13583,192.45,0.20398,0.4495,0.86968,-80.047,0.59609,0.64766,-0.47457,-8.05

> view matrix models
> #5,-0.77658,0.61521,-0.13583,190.52,0.20398,0.4495,0.86968,-80.75,0.59609,0.64766,-0.47457,-6.6014

> select ~sel & ##selected

Nothing selected  

> vop add #7 #5

Opened volume sum as #8, grid size 825,773,878, pixel 0.571, shown at step 1,
values float32  
Segmenting volume sum, density threshold 0.011667  
Showing 55 region surfaces  
264 watershed regions, grouped to 55 regions  
Showing volume sum.seg - 55 regions, 55 surfaces  

> select #3.15

1 model selected  

> select #3.44

1 model selected  

> select add #3.15

2 models selected  

> select add #3.43

3 models selected  
Drag select of 378, 21764 of 60816 triangles, 409, 10250 of 36460 triangles,
397, 5380 of 36504 triangles, 337, 2355 of 29204 triangles, 400, 12343 of
30684 triangles, 374, 7317 of 30628 triangles, 329, 8487 of 26008 triangles,
365, 2438 of 24424 triangles, 328, 11833 of 21756 triangles, 363, 8127 of
21104 triangles, 392, 14045 of 21212 triangles, 234, 329 of 12216 triangles, 8
volume sum  
Drag select of 378, 362, 460 of 47492 triangles, 388, 2905 of 38780 triangles,
409, 397, 402, 31179 of 31208 triangles, 400, 27132 of 30684 triangles, 374,
399, 3711 of 31532 triangles, 329, 11554 of 26008 triangles, 353, 4832 of
29064 triangles, 365, 2323 of 24424 triangles, 328, 15179 of 21756 triangles,
363, 17541 of 21104 triangles, 398, 11975 of 19464 triangles, 392, 12214 of
21212 triangles, 244, 15769 of 16880 triangles, 234, 2485 of 12216 triangles,
8 volume sum  

> select add #3.15

1 model selected  

> select add #3.44

2 models selected  

> select add #3.43

3 models selected  

> select add #3.50

4 models selected  
Drag select of 378, 2932 of 60816 triangles, 409, 2882 of 36460 triangles,
397, 1606 of 36504 triangles, 400, 672 of 30684 triangles, 328, 177 of 21756
triangles, 8 volume sum  

> select subtract #3.3

6 models selected  

> select subtract #3.27

5 models selected  

> select subtract #3.17

4 models selected  

> select subtract #3.44

3 models selected  

> select subtract #3.50

2 models selected  
Drag select of 378, 765 of 60816 triangles, 409, 1866 of 36460 triangles, 397,
1616 of 36504 triangles, 400, 1244 of 30684 triangles, 374, 41 of 30628
triangles, 328, 1311 of 21756 triangles, 8 volume sum  

> select add #3.24

7 models selected  

> select add #3.50

8 models selected  

> select add #3.44

9 models selected  

> select add #3.54

10 models selected  

> select add #3.48

11 models selected  

> select add #3.34

12 models selected  
Saving 43 regions to mrc file...  
Opened volume sum_43_regions.mrc as #9, grid size 168,194,211, pixel 0.571,
shown at step 1, values float32  
Wrote volume sum_43_regions.mrc  

> select subtract #3.13

42 models selected  

> select subtract #3.21

41 models selected  

> select subtract #3.36

40 models selected  

> select subtract #3.12

39 models selected  

> select subtract #3.19

38 models selected  

> select subtract #3.28

37 models selected  

> select subtract #3.46

36 models selected  

> select subtract #3.35

35 models selected  

> select subtract #3.25

34 models selected  

> select subtract #3.32

33 models selected  

> select subtract #3.47

32 models selected  

> select subtract #3.39

31 models selected  

> select subtract #3.49

30 models selected  

> select subtract #3.37

29 models selected  

> select subtract #3.40

28 models selected  

> select subtract #3.26

27 models selected  

> select subtract #3.55

26 models selected  

> select add #3.55

27 models selected  

> select subtract #3.55

26 models selected  

> ui tool show "Segment Map"

> hide #!4 models

> hide #!3 models

> select add #3

56 models selected  

> select subtract #3

Nothing selected  

> hide #!7 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> select add #9

57 models selected  

> volume #9 level 0.01212

> volume resample #9 onGrid #2

Opened volume sum_43_regions.mrc resampled as #10, grid size 500,500,500,
pixel 0.571, shown at step 1, values float32  

> hide #!10 models

> show #!10 models

> select subtract #9

55 models selected  

> select add #3

56 models selected  

> select subtract #3

Nothing selected  

> hide #!10 models

> show #!10 models

> show #!8 models

> hide #!10 models

> close #10

> volume resample #9 onGrid #1

Opened volume sum_43_regions.mrc resampled as #10, grid size 500,500,500,
pixel 0.571, shown at step 1, values float32  

> volume resample #8 onGrid #1

Opened volume sum resampled as #11, grid size 500,500,500, pixel 0.571, shown
at step 1, values float32  

> hide #!10 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!10 models

> save maskSUM.mrc #11

> save mask43regions.mrc #10

> save "/Users/maliona/Desktop/Cryo-EM/Factor XIa/Chimera Sessions/Making a
> map.cxs"

> hide #!10 models

> ui tool show "Segment Map"

Segmenting volume sum_43_regions.mrc, density threshold 0.012123  
Showing 43 region surfaces  
223 watershed regions, grouped to 43 regions  
Showing volume sum_43_regions.seg - 43 regions, 43 surfaces  

> select add #3.17

1 model selected  

> select add #3.37

2 models selected  

> select add #3.23

3 models selected  

> select add #3.22

4 models selected  

> select add #3.28

5 models selected  

> select add #3.26

6 models selected  

> select add #3.13

7 models selected  

> select add #3.12

8 models selected  

> select add #3.38

9 models selected  

> select add #3.32

10 models selected  
Drag select of 329, 4956 of 38168 triangles, 309, 8264 of 46568 triangles,
302, 5391 of 35064 triangles, 332, 525 of 31288 triangles, 318, 1136 of 28692
triangles  

> select add #3.17

6 models selected  

> select add #3.12

7 models selected  

> select add #3.28

8 models selected  

> select add #3.13

9 models selected  

> select add #3.18

10 models selected  

> select add #3.29

11 models selected  

> select add #3.30

12 models selected  

> select add #3.21

13 models selected  

> select add #3.26

14 models selected  

> select add #3.33

15 models selected  

> select add #3.39

16 models selected  

> select add #3.43

17 models selected  

> select add #3.35

18 models selected  

> select subtract #3.35

17 models selected  
Saving 26 regions to mrc file...  
Opened volume_26_regions.mrc as #12, grid size 161,171,167, pixel 0.571, shown
at step 1, values float32  
Wrote volume_26_regions.mrc  

> volume resample #12 onGrid #1

Opened volume_26_regions.mrc resampled as #13, grid size 500,500,500, pixel
0.571, shown at step 1, values float32  

> hide #!3 models

> select add #3

44 models selected  

> select subtract #3

Nothing selected  

> volume #13 level 0.03726

> volume #13 level 0.01072

> save mask26regions.mrc #13

> save "/Users/maliona/Desktop/Cryo-EM/Factor XIa/Chimera Sessions/Making a
> map.cxs" includeMaps true

——— End of log from Thu Nov 21 11:52:46 2024 ———

opened ChimeraX session  
Showing volume sum_43_regions.seg - 43 regions, 43 surfaces  

> hide #!13 models

> hide #!3 models

> show #!13 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!10 models

> show #!11 models

> hide #!10 models

> show #!10 models

> hide #!11 models

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #!3 models

> hide #!3 models

> show #!4 models

> select add #4

2 models selected  

> select subtract #4

Nothing selected  

> select add #5

2 models selected  

> show #!5 models

> hide #!4 models

> view matrix models
> #5,-0.77658,0.61521,-0.13583,172.91,0.20398,0.4495,0.86968,-92.272,0.59609,0.64766,-0.47457,130.91

> view matrix models
> #5,-0.77658,0.61521,-0.13583,152.17,0.20398,0.4495,0.86968,-86.17,0.59609,0.64766,-0.47457,148.22

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.43621,0.36071,-0.82439,152.34,0.13245,0.88042,0.45531,-65.827,0.89004,-0.3078,0.33627,104.52

> view matrix models
> #5,0.84525,0.4268,-0.32154,-3.9403,-0.37645,0.90266,0.20856,44.112,0.37926,-0.055243,0.92364,28.628

> view matrix models
> #5,0.95971,0.14351,-0.24158,8.5861,-0.16468,0.98388,-0.069735,54.035,0.22767,0.10671,0.96787,16.707

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.95971,0.14351,-0.24158,-5.0365,-0.16468,0.98388,-0.069735,26.097,0.22767,0.10671,0.96787,-22.246

> view matrix models
> #5,0.95971,0.14351,-0.24158,25.851,-0.16468,0.98388,-0.069735,42.466,0.22767,0.10671,0.96787,-28.656

> view matrix models
> #5,0.95971,0.14351,-0.24158,24.428,-0.16468,0.98388,-0.069735,36.766,0.22767,0.10671,0.96787,-41.128

> view matrix models
> #5,0.95971,0.14351,-0.24158,24.852,-0.16468,0.98388,-0.069735,37.5,0.22767,0.10671,0.96787,-39.951

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.75962,0.36431,-0.53876,72.676,-0.32803,0.92991,0.1663,24.662,0.56158,0.050402,0.82589,-50.614

> view matrix models
> #5,0.75209,0.35965,-0.55227,76.842,-0.33296,0.93052,0.15254,27.735,0.56876,0.069163,0.81959,-53.246

> view matrix models
> #5,0.65589,0.42432,-0.62431,93.178,-0.38002,0.90021,0.21259,27.692,0.65222,0.097814,0.75169,-56.425

> view matrix models
> #5,0.95745,-0.039435,-0.28589,60.623,0.025286,0.99827,-0.053014,6.76,0.28749,0.043529,0.95679,-36.514

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.95745,-0.039435,-0.28589,64.275,0.025286,0.99827,-0.053014,10.319,0.28749,0.043529,0.95679,-43.279

> view matrix models
> #5,0.95745,-0.039435,-0.28589,61.586,0.025286,0.99827,-0.053014,15.804,0.28749,0.043529,0.95679,-41.8

> vop add #5 #8

Opened volume sum as #14, grid size 1064,844,1119, pixel 0.571, shown at step
1, values float32  

> select subtract #5

Nothing selected  

> show #!8 models

> volume #14 style mesh

> volume #14 level 0.02732

> hide #!8 models

> volume #14 level 0.0417

> volume #14 level 0.03895

> volume #14 style surface

> volume #14 level 0.03099

> volume #14 level 0.02281

> show #!5 models

> select add #5

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.95745,-0.039435,-0.28589,54.662,0.025286,0.99827,-0.053014,-0.87368,0.28749,0.043529,0.95679,-38.909

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.90693,0.11916,-0.40408,59.166,-0.16149,0.98423,-0.07221,29.835,0.3891,0.13074,0.91187,-57.478

> view matrix models
> #5,0.8368,0.26519,-0.47901,60.333,-0.30356,0.95281,-0.0028091,41.037,0.45566,0.14776,0.87781,-62.788

> view matrix models
> #5,0.84036,0.2888,-0.45867,52.619,-0.34449,0.93791,-0.040614,55.643,0.41847,0.19214,0.88768,-66.231

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.84036,0.2888,-0.45867,-13.07,-0.34449,0.93791,-0.040614,35.931,0.41847,0.19214,0.88768,-12.104

> view matrix models
> #5,0.84036,0.2888,-0.45867,63.606,-0.34449,0.93791,-0.040614,32.783,0.41847,0.19214,0.88768,-36.367

> view matrix models
> #5,0.84036,0.2888,-0.45867,62.399,-0.34449,0.93791,-0.040614,54.854,0.41847,0.19214,0.88768,-53.858

> view matrix models
> #5,0.84036,0.2888,-0.45867,63.561,-0.34449,0.93791,-0.040614,53.724,0.41847,0.19214,0.88768,-58.743

> view matrix models
> #5,0.84036,0.2888,-0.45867,63.986,-0.34449,0.93791,-0.040614,52.017,0.41847,0.19214,0.88768,-58.615

> view matrix models
> #5,0.84036,0.2888,-0.45867,65.401,-0.34449,0.93791,-0.040614,51.644,0.41847,0.19214,0.88768,-62.375

> view matrix models
> #5,0.84036,0.2888,-0.45867,66.098,-0.34449,0.93791,-0.040614,51.291,0.41847,0.19214,0.88768,-63.899

> vop add #5 #14

Opened volume sum as #15, grid size 1479,1226,1312, pixel 0.571, shown at step
1, values float32  

> select subtract #5

Nothing selected  

> show #!5 models

> select add #5

2 models selected  

> view matrix models
> #5,0.84036,0.2888,-0.45867,104.57,-0.34449,0.93791,-0.040614,43.26,0.41847,0.19214,0.88768,-212.4

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.92823,-0.085318,0.36208,249.31,-0.18498,0.95034,-0.25027,58.045,-0.32275,-0.29929,-0.89792,285.37

> view matrix models
> #5,-0.86059,0.071564,0.50425,190.87,-0.21091,0.85112,-0.48075,118.28,-0.46358,-0.52007,-0.71737,304.59

> view matrix models
> #5,-0.62409,0.25767,0.73765,88.771,-0.43704,0.66746,-0.60291,198.41,-0.6477,-0.69865,-0.30394,280.98

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.62409,0.25767,0.73765,54.58,-0.43704,0.66746,-0.60291,221.3,-0.6477,-0.69865,-0.30394,296.77

> view matrix models
> #5,-0.62409,0.25767,0.73765,59.875,-0.43704,0.66746,-0.60291,221.57,-0.6477,-0.69865,-0.30394,328.69

> view matrix models
> #5,-0.62409,0.25767,0.73765,60.889,-0.43704,0.66746,-0.60291,222.88,-0.6477,-0.69865,-0.30394,324.21

> view matrix models
> #5,-0.62409,0.25767,0.73765,67.512,-0.43704,0.66746,-0.60291,221.06,-0.6477,-0.69865,-0.30394,325.77

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.091059,-0.87315,-0.47887,386.34,-0.77418,0.36453,-0.51745,296.26,0.62638,0.32361,-0.70917,74.9

> vop add #5 #15

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3234, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3870, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 336, in volume_add  
rv = combine_op(volumes, 'add', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\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 1.8\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 1.8\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 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close #6

> close #7

> close #14

> vop add #5 #15

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3234, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3870, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 336, in volume_add  
rv = combine_op(volumes, 'add', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\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 1.8\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 1.8\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 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> vop add #5 #15

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3234, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3870, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 336, in volume_add  
rv = combine_op(volumes, 'add', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\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 1.8\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 1.8\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 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> vop add #5 #15

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3234, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3870, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 336, in volume_add  
rv = combine_op(volumes, 'add', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\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 1.8\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 1.8\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 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> vop add #5 #15

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3234, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3870, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 336, in volume_add  
rv = combine_op(volumes, 'add', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\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 1.8\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 1.8\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 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> vop add #5 #15

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3234, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3870, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 336, in volume_add  
rv = combine_op(volumes, 'add', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\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 1.8\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 1.8\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 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 40.1 GiB for an
array with shape (2215, 2141, 2271) and data type float32  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1061, in region_grid  
m = zeros(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 22.20.42.02.221103
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_DE.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: Vivobook Go E1504FA_E1504FA
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,407,719,936
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 5 7520U with Radeon Graphics         
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

[Tom Goddard]

Out of memory allocating a volume from volume add command. Working with many large volumes ~800 x 800 x 800 and on Windows 10 machine with only 16 GB. Seems Windows 10 is the common ingredient of all the out of memory errors.