Save MRC: could not broadcast input array

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.7.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/heteroX_3,26.mrc

Opened heteroX_3,26.mrc as #1, grid size 290,290,290, pixel 0.86, shown at
level 0.0145, step 2, values float32  

> open
> /Users/surimsoh/Documents/RsCas9/fold_drscas9_ternery_complex_mg2/fold_drscas9_ternery_complex_mg2_model_4.cif

Chain information for fold_drscas9_ternery_complex_mg2_model_4.cif #2  
---  
Chain | Description  
A | .  
D | .  
E | .  
F | .  
  
Computing secondary structure  

> open
> /Users/surimsoh/Documents/RsCas9/fold_drscas9_ternery_complex_mg3/fold_drscas9_ternery_complex_mg3_model_4.cif

Chain information for fold_drscas9_ternery_complex_mg3_model_4.cif #3  
---  
Chain | Description  
A | .  
E | .  
F | .  
G | .  
  
Computing secondary structure  

> close #2

> select add #3

14012 atoms, 14771 bonds, 1383 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,61.057,0,1,0,129.41,0,0,1,170.33

> view matrix models #3,1,0,0,123.32,0,1,0,142.39,0,0,1,151.97

> view matrix models #3,1,0,0,118.09,0,1,0,124.37,0,0,1,129.45

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.99768,0.049384,-0.04692,117.3,-0.063182,0.9283,-0.36642,116.96,0.02546,0.36854,0.92926,129

> view matrix models
> #3,0.97095,-0.030143,-0.23739,113.26,-0.055782,0.93619,-0.34703,117.37,0.2327,0.35019,0.90731,128.07

> view matrix models
> #3,-0.88654,0.46249,-0.012118,121.57,-0.35581,-0.69831,-0.6211,105.55,-0.29571,-0.54632,0.78364,122.89

> view matrix models
> #3,-0.88791,0.4526,-0.082261,120.11,-0.15739,-0.46693,-0.87018,100.98,-0.43225,-0.75969,0.48582,116.29

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.88791,0.4526,-0.082261,123.84,-0.15739,-0.46693,-0.87018,125.13,-0.43225,-0.75969,0.48582,125.15

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.96878,0.22477,-0.10459,122.8,-0.02312,-0.50196,-0.86458,124.94,-0.24683,-0.83517,0.49149,124.77

> view matrix models
> #3,-0.96238,0.25146,-0.10287,122.91,-0.039573,-0.50432,-0.86261,125,-0.26879,-0.82609,0.4953,124.91

> volume flip #1

Opened heteroX_3,26.mrc z flip as #2, grid size 290,290,290, pixel 0.86, shown
at step 1, values float32  

> close #1

> view matrix models
> #3,-0.95245,0.24546,0.18053,128.55,0.14085,0.88006,-0.45349,137.81,-0.27019,-0.40649,-0.87279,98.988

> view matrix models
> #3,-0.92415,0.021537,-0.38143,116.02,0.030131,0.99941,-0.016572,147.26,0.38085,-0.026808,-0.92425,98.208

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.92415,0.021537,-0.38143,118.53,0.030131,0.99941,-0.016572,117.91,0.38085,-0.026808,-0.92425,126.2

> ui mousemode right "rotate selected models"

> surface dust #2 size 8.6

> view matrix models
> #3,-0.89774,0.24744,-0.36447,119.66,0.42244,0.71819,-0.55295,105.3,0.12493,-0.65037,-0.74927,128.52

> view matrix models
> #3,0.92281,-0.30248,-0.23859,116.52,-0.35171,-0.40873,-0.84216,96.032,0.15721,0.86107,-0.48357,140.32

> view matrix models
> #3,0.93743,-0.2562,-0.23576,116.69,-0.30338,-0.26883,-0.91416,94.887,0.17083,0.92849,-0.32974,143.62

> view matrix models
> #3,0.89315,-0.39242,-0.21975,116.67,-0.43709,-0.64217,-0.62973,99.776,0.106,0.6585,-0.74508,134.37

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.89315,-0.39242,-0.21975,117.61,-0.43709,-0.64217,-0.62973,113.41,0.106,0.6585,-0.74508,115.69

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.92118,-0.30756,-0.2384,117.46,-0.35685,-0.42332,-0.83274,109.84,0.1552,0.85218,-0.4997,121.3

> view matrix models
> #3,0.9243,-0.28263,-0.25649,117.18,-0.34969,-0.35789,-0.86581,109.36,0.15291,0.88996,-0.42963,122.84

> undo

> view matrix models
> #3,0.86325,-0.4449,-0.23846,117.16,-0.42049,-0.37245,-0.82733,110.29,0.27927,0.81446,-0.50859,120.66

> fitmap #3 inMap #2

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#3) to map
heteroX_3,26.mrc z flip (#2) using 14012 atoms  
average map value = 0.008579, steps = 120  
shifted from previous position = 2.14  
rotated from previous position = 7.62 degrees  
atoms outside contour = 10496, contour level = 0.014507  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#3) relative to
heteroX_3,26.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.80388483 -0.53850659 -0.25254670 116.32206719  
-0.45369826 -0.28061241 -0.84582183 110.71249653  
0.38461288 0.79452334 -0.46989956 122.70246685  
Axis 0.93106840 -0.36165508 0.04813765  
Axis point 0.00000000 39.69650640 102.50487180  
Rotation angle (degrees) 118.24960349  
Shift along axis 74.17067262  
  

> view matrix models
> #3,0.81986,-0.51939,-0.24094,116.58,-0.41767,-0.2547,-0.87217,110.18,0.39163,0.81569,-0.42576,123.65

> fitmap #3 inMap #2

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#3) to map
heteroX_3,26.mrc z flip (#2) using 14012 atoms  
average map value = 0.008579, steps = 84  
shifted from previous position = 1.08  
rotated from previous position = 3.11 degrees  
atoms outside contour = 10496, contour level = 0.014507  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#3) relative to
heteroX_3,26.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.80380442 -0.53856398 -0.25268023 116.32390992  
-0.45385783 -0.28057805 -0.84574762 110.71690303  
0.38459268 0.79449657 -0.46996136 122.70305037  
Axis 0.93104171 -0.36173130 0.04808123  
Axis point 0.00000000 39.70422446 102.50785383  
Rotation angle (degrees) 118.25311087  
Shift along axis 74.15235685  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.8038,-0.53856,-0.25268,121.17,-0.45386,-0.28058,-0.84575,125.37,0.38459,0.7945,-0.46996,119.61

> fitmap #3 inMap #2

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#3) to map
heteroX_3,26.mrc z flip (#2) using 14012 atoms  
average map value = 0.01033, steps = 252  
shifted from previous position = 5.46  
rotated from previous position = 9.81 degrees  
atoms outside contour = 9804, contour level = 0.014507  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#3) relative to
heteroX_3,26.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.82021038 -0.56520750 -0.08829166 124.95374309  
-0.32367028 -0.33125127 -0.88629010 122.54870476  
0.47169109 0.75552173 -0.45463660 122.47888708  
Axis 0.93741831 -0.31973096 0.13790948  
Axis point 0.00000000 48.12359145 100.20210728  
Rotation angle (degrees) 118.87096961  
Shift along axis 94.84231026  
  

> select add #2

14012 atoms, 14771 bonds, 1383 residues, 3 models selected  

> save
> /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/13,26/heteroX_3,26.mrc
> models #2

> save
> /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/13,26/heteroX_3,26.pdb
> displayedOnly true selectedOnly true relModel #2

> close #3

> open
> /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/13,26/heteroX_3,26.pdb

Summary of feedback from opening
/Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/13,26/heteroX_3,26.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 59 ARG A 89 1 31  
Start residue of secondary structure not found: HELIX 2 2 THR A 97 ALA A 102 1
6  
Start residue of secondary structure not found: HELIX 3 3 LEU A 103 GLY A 105
1 3  
Start residue of secondary structure not found: HELIX 4 4 PRO A 108 ALA A 113
1 6  
Start residue of secondary structure not found: HELIX 5 5 ARG A 114 LEU A 116
1 3  
90 messages similar to the above omitted  
  
Chain information for heteroX_3,26.pdb #1  
---  
Chain | Description  
A | No description available  
E | No description available  
F | No description available  
G | No description available  
  
Computing secondary structure  

> select /A:663-1115

61 atoms, 55 bonds, 6 pseudobonds, 7 residues, 2 models selected  

> close #1

> open
> /Users/surimsoh/Documents/RsCas9/fold_drscas9_ternery_complex_mg3/fold_drscas9_ternery_complex_mg3_model_4.cif

Chain information for fold_drscas9_ternery_complex_mg3_model_4.cif #1  
---  
Chain | Description  
A | .  
E | .  
F | .  
G | .  
  
Computing secondary structure  

> select add #1

14012 atoms, 14771 bonds, 1383 residues, 1 model selected  

> view matrix models #1,1,0,0,111.03,0,1,0,122.26,0,0,1,121.41

> view matrix models #1,1,0,0,112.2,0,1,0,124.4,0,0,1,134.93

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99977,-0.0055959,-0.02052,111.67,0.0062305,0.9995,0.030994,125.14,0.020336,-0.031114,0.99931,134.71

> view matrix models
> #1,0.9889,-0.025498,-0.14639,109.1,0.056643,0.97547,0.21272,128.61,0.13738,-0.21865,0.96608,133.18

> view matrix models
> #1,0.72107,-0.66841,-0.18243,106.75,-0.43353,-0.22988,-0.87132,103.36,0.54046,0.70738,-0.45554,106.31

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.72107,-0.66841,-0.18243,112.53,-0.43353,-0.22988,-0.87132,133.34,0.54046,0.70738,-0.45554,125.76

> view matrix models
> #1,0.72107,-0.66841,-0.18243,116.45,-0.43353,-0.22988,-0.87132,134.23,0.54046,0.70738,-0.45554,124.49

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.8903,0.44599,-0.091955,125.06,0.44388,0.80486,-0.39391,146.27,-0.10167,-0.39152,-0.91454,112.2

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.8903,0.44599,-0.091955,123.56,0.44388,0.80486,-0.39391,136.29,-0.10167,-0.39152,-0.91454,120.72

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.96268,-0.25251,-0.097367,118.04,-0.2112,-0.47603,-0.85369,122.41,0.16921,0.8424,-0.5116,133.75

> view matrix models
> #1,0.85267,-0.48686,-0.18956,115.63,-0.42192,-0.42769,-0.79941,124.12,0.30813,0.76161,-0.57009,132.01

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.85267,-0.48686,-0.18956,128.8,-0.42192,-0.42769,-0.79941,124.8,0.30813,0.76161,-0.57009,127.12

> fitmap #1 inMap #2

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#1) to map
heteroX_3,26.mrc (#2) using 14012 atoms  
average map value = 0.01048, steps = 136  
shifted from previous position = 3.92  
rotated from previous position = 4.69 degrees  
atoms outside contour = 9903, contour level = 0.014507  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#1) relative to
heteroX_3,26.mrc (#2) coordinates:  
Matrix rotation and translation  
0.83324418 -0.50694531 -0.22070476 126.84584014  
-0.43410315 -0.35260610 -0.82898938 123.27803516  
0.34243043 0.78655921 -0.51387353 124.15701791  
Axis 0.94342332 -0.32885107 0.04253725  
Axis point 0.00000000 47.67224835 104.40995846  
Rotation angle (degrees) 121.10564772  
Shift along axis 84.41050815  
  

> select add #2

14012 atoms, 14771 bonds, 1383 residues, 3 models selected  

> save
> /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/13,26/heteroX_3,26.pdb
> selectedOnly true relModel #2

> open
> /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/13,26/heteroX_3,26.pdb
> /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/13,26/heteroX_3,26.mrc

Chain information for heteroX_3,26.pdb #3  
---  
Chain | Description  
A | No description available  
E | No description available  
F | No description available  
G | No description available  
  
Opened heteroX_3,26.mrc as #4, grid size 290,290,290, pixel 0.86, shown at
level 0.0145, step 2, values float32  

> close #1,3#2,4

> open /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/3v_hetero_3,32.mrc

Opened 3v_hetero_3,32.mrc as #1, grid size 290,290,290, pixel 0.86, shown at
level 0.0157, step 2, values float32  

> open
> /Users/surimsoh/Documents/RsCas9/fold_drscas9_ternery_complex_mg3/fold_drscas9_ternery_complex_mg3_model_4.cif

Chain information for fold_drscas9_ternery_complex_mg3_model_4.cif #2  
---  
Chain | Description  
A | .  
E | .  
F | .  
G | .  
  
Computing secondary structure  

> select add #2

14012 atoms, 14771 bonds, 1383 residues, 1 model selected  

> view matrix models #2,1,0,0,102.56,0,1,0,150.06,0,0,1,143.67

> view matrix models #2,1,0,0,137.06,0,1,0,131.3,0,0,1,113.54

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.31773,0.92037,0.22794,147.2,0.86961,0.37868,-0.31684,121.11,-0.37792,0.09755,-0.92068,74.65

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.31773,0.92037,0.22794,136.72,0.86961,0.37868,-0.31684,123.21,-0.37792,0.09755,-0.92068,114.44

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.68931,0.7136,0.12499,134.73,0.65438,0.68732,-0.31524,124.79,-0.31086,-0.13551,-0.94075,113.07

> view matrix models
> #2,-0.65449,0.7458,0.12422,134.74,0.68005,0.65249,-0.33435,124.26,-0.33041,-0.13435,-0.93423,113.24

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.65449,0.7458,0.12422,131.97,0.68005,0.65249,-0.33435,126.36,-0.33041,-0.13435,-0.93423,116.12

> fitmap #2 inMap #1

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#2) to map
3v_hetero_3,32.mrc (#1) using 14012 atoms  
average map value = 0.01693, steps = 264  
shifted from previous position = 11.7  
rotated from previous position = 4.32 degrees  
atoms outside contour = 9920, contour level = 0.015726  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#2) relative to
3v_hetero_3,32.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.67606706 0.71468170 0.17934154 141.60965393  
0.63159309 0.68743148 -0.35850820 131.43358512  
-0.37950427 -0.12910471 -0.91613781 111.82876584  
Axis 0.37620360 0.91646298 -0.13625876  
Axis point 55.19608220 0.00000000 58.70001930  
Rotation angle (degrees) 162.24828914  
Shift along axis 158.49042850  
  

> view matrix models
> #2,-0.67607,0.71468,0.17934,124.14,0.63159,0.68743,-0.35851,133.46,-0.3795,-0.1291,-0.91614,111.64

> volume flip #1

Opened 3v_hetero_3,32.mrc z flip as #3, grid size 290,290,290, pixel 0.86,
shown at step 1, values float32  

> close #1

> surface dust #3 size 8.6

> fitmap #2 inMap #3

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#2) to map
3v_hetero_3,32.mrc z flip (#3) using 14012 atoms  
average map value = 0.009547, steps = 180  
shifted from previous position = 7.6  
rotated from previous position = 7.14 degrees  
atoms outside contour = 10561, contour level = 0.015726  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#2) relative to
3v_hetero_3,32.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.71786247 0.64238355 0.26835956 128.96492003  
0.56617313 0.76299693 -0.31190331 128.62946760  
-0.40511908 -0.07196571 -0.91142716 114.84920145  
Axis 0.33371320 0.93669651 -0.10599599  
Axis point 54.56242481 0.00000000 56.91426390  
Rotation angle (degrees) 158.93070912  
Shift along axis 151.35051491  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.47407,-0.44143,0.76184,134.86,-0.044445,-0.85215,-0.52141,120.29,0.87937,-0.28104,0.38435,137.75

> view matrix models
> #2,-0.86325,-0.47878,-0.15993,116.29,0.48053,-0.6824,-0.55084,119.38,0.15459,-0.55236,0.81915,147.05

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.86325,-0.47878,-0.15993,122.63,0.48053,-0.6824,-0.55084,129.32,0.15459,-0.55236,0.81915,127.59

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.78077,-0.50879,0.36267,128.89,0.60515,0.76026,-0.23622,139.69,-0.15554,0.40391,0.90148,132.92

> view matrix models
> #2,0.85372,-0.51431,0.081506,123.06,0.51711,0.81892,-0.24894,139.74,0.061285,0.25467,0.96508,133.44

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.85372,-0.51431,0.081506,131.12,0.51711,0.81892,-0.24894,137.92,0.061285,0.25467,0.96508,140.39

> fitmap #2 inMap #3

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#2) to map
3v_hetero_3,32.mrc z flip (#3) using 14012 atoms  
average map value = 0.0102, steps = 256  
shifted from previous position = 6.47  
rotated from previous position = 10.9 degrees  
atoms outside contour = 10517, contour level = 0.015726  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#2) relative to
3v_hetero_3,32.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.83424230 -0.54864115 -0.05506985 125.64061498  
0.53941960 0.83274323 -0.12476063 135.09986037  
0.11430786 0.07437484 0.99065741 138.04040344  
Axis 0.17795423 -0.15136168 0.97232810  
Axis point -211.52144004 248.75464415 0.00000000  
Rotation angle (degrees) 34.02213654  
Shift along axis 136.12989992  
  

> view matrix models
> #2,0.83424,-0.54864,-0.05507,116.25,0.53942,0.83274,-0.12476,131.61,0.11431,0.074375,0.99066,140.46

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.61111,0.51952,0.59719,135.89,-0.68326,-0.72712,-0.066635,127.7,0.39961,-0.44876,0.79933,133.98

> view matrix models
> #2,-0.92831,0.35953,-0.094725,121.71,-0.13517,-0.56369,-0.81485,111.82,-0.34636,-0.74363,0.57188,129.68

> select ~sel & ##selected

Nothing selected  

> volume flip #3

Opened 3v_hetero_3,32.mrc z flip z flip as #1, grid size 290,290,290, pixel
0.86, shown at step 1, values float32  

> surface dust #1 size 8.6

> select add #2

14012 atoms, 14771 bonds, 1383 residues, 1 model selected  

> view matrix models
> #2,-0.73862,0.66309,0.12149,126.73,0.60129,0.7295,-0.326,124.65,-0.30479,-0.16774,-0.93753,101.23

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.73862,0.66309,0.12149,127.27,0.60129,0.7295,-0.326,130.03,-0.30479,-0.16774,-0.93753,115.99

> fitmap #2 inMap #1

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#2) to map
3v_hetero_3,32.mrc z flip z flip (#1) using 14012 atoms  
average map value = 0.01068, steps = 112  
shifted from previous position = 4.21  
rotated from previous position = 3.72 degrees  
atoms outside contour = 10168, contour level = 0.015726  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#2) relative to
3v_hetero_3,32.mrc z flip z flip (#1) coordinates:  
Matrix rotation and translation  
-0.73803093 0.67166424 0.06463354 130.59131748  
0.61151510 0.70626410 -0.35670760 131.11598356  
-0.28523609 -0.22373685 -0.93197757 118.21852166  
Axis 0.35076462 0.92292398 -0.15866791  
Axis point 47.72228286 0.00000000 66.30443513  
Rotation angle (degrees) 169.07381910  
Shift along axis 148.05941432  
  

> close #3

> select add #1

14012 atoms, 14771 bonds, 1383 residues, 3 models selected  

> save /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/3v_hetero_3,32.mrc
> models #1

> save /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/3v_hetero_3,32.pdb
> selectedOnly true relModel #1

> undo

> open /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/2v_hetero_3,30.mrc

Opened 2v_hetero_3,30.mrc as #3, grid size 290,290,290, pixel 0.86, shown at
level 0.0159, step 2, values float32  

> close #1

> surface dust #3 size 8.6

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.63473,0.7097,0.30568,135.33,-0.74327,-0.45255,-0.49269,127.11,-0.21132,-0.53993,0.81475,151.86

> select ~sel & ##selected

Nothing selected  

> volume flip #3

Opened 2v_hetero_3,30.mrc z flip as #1, grid size 290,290,290, pixel 0.86,
shown at step 1, values float32  

> surface dust #1 size 8.6

> select add #2

14012 atoms, 14771 bonds, 1383 residues, 1 model selected  

> view matrix models
> #2,-0.90912,0.044879,-0.41411,119.62,0.36271,0.57409,-0.73407,122.82,0.20479,-0.81756,-0.53819,122.77

> view matrix models
> #2,-0.94109,0.30687,-0.14207,126.27,0.33794,0.86844,-0.36278,131.64,0.012052,-0.38942,-0.92098,116.72

> view matrix models
> #2,-0.7311,0.5814,0.35701,136.65,0.49708,0.81234,-0.30497,132.33,-0.46733,-0.0455,-0.88291,119.54

> view matrix models
> #2,-0.78028,0.60589,0.15508,132.79,0.55618,0.78563,-0.27101,132.79,-0.28604,-0.12521,-0.95,117.33

> view matrix models
> #2,-0.76803,0.6222,0.15165,132.75,0.54926,0.76174,-0.34361,131.29,-0.32931,-0.18061,-0.92679,117.71

> fitmap #2 inMap #1

Fit molecule fold_drscas9_ternery_complex_mg3_model_4.cif (#2) to map
2v_hetero_3,30.mrc z flip (#1) using 14012 atoms  
average map value = 0.0114, steps = 180  
shifted from previous position = 2.05  
rotated from previous position = 4.67 degrees  
atoms outside contour = 10132, contour level = 0.015894  
  
Position of fold_drscas9_ternery_complex_mg3_model_4.cif (#2) relative to
2v_hetero_3,30.mrc z flip (#1) coordinates:  
Matrix rotation and translation  
-0.76724541 0.63534130 0.08761239 130.67350231  
0.58738766 0.75094708 -0.30175191 131.32504096  
-0.25750772 -0.18005533 -0.94935234 117.73249578  
Axis 0.32973263 0.93509087 -0.12992869  
Axis point 49.01534555 0.00000000 63.95806363  
Rotation angle (degrees) 169.36578596  
Shift along axis 150.59133521  
  

> select add #1

14012 atoms, 14771 bonds, 1383 residues, 3 models selected  

> close #3

> save /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/2v_hetero_3,30.mrc
> models #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 200, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4028, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 326, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/writemrc.py", line 73, in
write_mrc2000_grid_data  
matrix = grid_data.matrix((0,0,k), (isz,jsz,1))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 39, in matrix  
m = self.data.matrix(origin, ijk_size, ijk_step, progress=progress,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 50, in read_matrix  
m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 287, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: could not broadcast input array from shape (0,) into shape (290,)  
  
ValueError: could not broadcast input array from shape (0,) into shape (290,)  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> save /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/2v_hetero_3,30.mrc
> models #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 200, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4028, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 326, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/writemrc.py", line 73, in
write_mrc2000_grid_data  
matrix = grid_data.matrix((0,0,k), (isz,jsz,1))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 39, in matrix  
m = self.data.matrix(origin, ijk_size, ijk_step, progress=progress,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 50, in read_matrix  
m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 287, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: could not broadcast input array from shape (0,) into shape (290,)  
  
ValueError: could not broadcast input array from shape (0,) into shape (290,)  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select subtract #2

2 models selected  

> save
> /Users/surimsoh/Documents/RsCas9/251028_re_Topaz/re/2v_hetero_3,30_1.mrc
> models #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 200, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4028, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 326, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/writemrc.py", line 73, in
write_mrc2000_grid_data  
matrix = grid_data.matrix((0,0,k), (isz,jsz,1))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 39, in matrix  
m = self.data.matrix(origin, ijk_size, ijk_step, progress=progress,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 50, in read_matrix  
m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 287, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: could not broadcast input array from shape (0,) into shape (290,)  
  
ValueError: could not broadcast input array from shape (0,) into shape (290,)  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,10
      Model Number: Z1740003QKH/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.1 (24G231)
      Kernel Version: Darwin 24.6.0
      Time since boot: 1일 7시간 59분

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    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
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    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: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

Similar to #9241

[Tom Goddard]

Saving a flipped map over itself. Fixed a month ago. Same as #18992.