measure center: Array argument has non-numeric values

[endang-purba@…]

The following bug report has been submitted:
Platform:        macOS-15.3.1-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Volumes/PegasusP32T_H29_04/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/cluster01_gauss_ave07.cxs

Opened cluster01_gauss_ave07.map.mrc as #1, grid size 75,75,75, pixel 1.75,
shown at level 5.44, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #5, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #6, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #7, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #8, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 as #11, grid size
28,31,33, pixel 3.33, shown at level 0.0494, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #9, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #10, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Opened fold_2025_05_19_synaptotagmin_140_422_model_0.cif map 10 as #12, grid
size 38,33,35, pixel 3.33, shown at level 0.0583, step 1, values float32  
Opened fold_2025_05_19_synaptotagmin_140_422_model_0.cif map 10 as #13, grid
size 38,33,35, pixel 3.33, shown at level 0.0583, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #14, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #15, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 as #16, grid size
28,31,33, pixel 3.33, shown at level 0.0494, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 as #17, grid size
28,31,33, pixel 3.33, shown at level 0.0494, step 1, values float32  
Log from Thu Feb 12 15:20:18 2026UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Volumes/PegasusP32T_H29_04/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/fitting_cluster01_gauss_ave07.cxs

Opened cluster01_gauss_ave07.map.mrc as #1, grid size 75,75,75, pixel 1.75,
shown at level 5.44, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #5, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #6, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #7, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #8, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 as #11, grid size
28,31,33, pixel 3.33, shown at level 0.0494, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #9, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #10, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Log from Fri Feb 6 16:30:53 2026UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Volumes/PegasusP32T_H29_04/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/fitting_cluster01_gauss_ave07.cxs

Opened cluster01_gauss_ave07.map.mrc as #1, grid size 75,75,75, pixel 1.75,
shown at level 5.44, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #5, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #6, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #7, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #8, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Log from Fri Feb 6 16:10:03 2026 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/PegasusP32T_H29_04/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/cluster01_gauss_ave07.map

MRC header value nsymbt (-89582272) is invalid  

> help help:user/preferences.html#startup

> open
> /Volumes/PegasusP32T_H29_04/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/cluster01_gauss_ave07.map.mrc

Opened cluster01_gauss_ave07.map.mrc as #1, grid size 75,75,75, pixel 1.75,
shown at level 5.44, step 1, values float32  

> volume #1 level 5.444

> open
> /Users/rina/Desktop/3_COMET_WORK_2023/alphafold_synaptotagmin/fold_2025_05_19_synaptotagmin_140_422/fold_2025_05_19_synaptotagmin_140_422_model_0.cif

Chain information for fold_2025_05_19_synaptotagmin_140_422_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  
Drag select of 1 cluster01_gauss_ave07.map.mrc , 283 residues  

> select clear

> ui mousemode right "translate selected models"

> select clear

> select #1

2 models selected  

> view matrix models #1,1,0,0,-83.261,0,1,0,-32.048,0,0,1,-9.4041

> view matrix models #1,1,0,0,-67.277,0,1,0,-61.511,0,0,1,-47.566

> volume #1 level 5.432

> select #1

2 models selected  

> transparency #1.1 50

> volume #1 level 5.436

> open
> /Users/rina/Desktop/3_COMET_WORK_2023/alphafold_synaptotagmin/fold_2025_08_07_syanptotagmin_c2a/fold_2025_08_07_syanptotagmin_c2a_model_0.cif

Chain information for fold_2025_08_07_syanptotagmin_c2a_model_0.cif #3  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #2 models

> view matrix models #1,1,0,0,-83.516,0,1,0,-61.417,0,0,1,-53.704

> view matrix models #1,1,0,0,-85.472,0,1,0,-63.266,0,0,1,-51.824

> view matrix models #1,1,0,0,-81.095,0,1,0,-62.781,0,0,1,-50.61

> select subtract #1

Nothing selected  

> select add #3

1024 atoms, 1049 bonds, 125 residues, 1 model selected  

> view matrix models #3,1,0,0,0.96729,0,1,0,-0.16312,0,0,1,1.1097

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.86565,0.12856,-0.48386,3.6141,-0.17722,0.98258,-0.055998,-0.030443,0.46823,0.13423,0.87335,2.3431

> view matrix models
> #3,0.97118,-0.040078,-0.23495,2.4526,-0.19164,0.45476,-0.86975,5.8015,0.1417,0.88971,0.43397,3.53

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.97118,-0.040078,-0.23495,-20.594,-0.19164,0.45476,-0.86975,11.425,0.1417,0.88971,0.43397,-9.8379

> view matrix models
> #3,0.97118,-0.040078,-0.23495,-19.619,-0.19164,0.45476,-0.86975,11.17,0.1417,0.88971,0.43397,-9.3449

> view matrix models
> #3,0.97118,-0.040078,-0.23495,-26.52,-0.19164,0.45476,-0.86975,1.3468,0.1417,0.88971,0.43397,-2.7683

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.96308,-0.012803,-0.26891,-26.359,-0.19997,0.63474,-0.74641,0.30176,0.18024,0.77262,0.60874,-3.6344

> view matrix models
> #3,0.92251,-0.012139,-0.38579,-25.686,-0.27018,0.69349,-0.66789,-0.37031,0.27565,0.72037,0.63647,-3.6003

> view matrix models
> #3,0.93505,-0.026782,-0.35351,-25.849,-0.26036,0.62492,-0.736,0.16866,0.24063,0.78023,0.57735,-3.3672

> view matrix models
> #3,0.81389,-0.52932,-0.2396,-25.988,0.12584,0.56318,-0.8167,1.2907,0.56723,0.63455,0.52497,-2.3801

> view matrix models
> #3,0.89385,-0.31084,0.32313,-29.711,0.44452,0.70866,-0.54791,-0.16411,-0.058677,0.63339,0.77161,-4.773

> open
> /Users/rina/Desktop/3_COMET_WORK_2023/alphafold_synaptotagmin/fold_2025_08_07_synaptotagmin_c2b/fold_2025_08_07_synaptotagmin_c2b_model_0.cif

Chain information for fold_2025_08_07_synaptotagmin_c2b_model_0.cif #4  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select subtract #3

Nothing selected  

> select add #4

1193 atoms, 1216 bonds, 149 residues, 1 model selected  

> view matrix models
> #4,0.58457,-0.49405,0.64358,2.0818,0.27956,0.8673,0.41186,1.7375,-0.76166,-0.060848,0.64512,-1.884

> view matrix models
> #4,0.26455,0.25428,0.93024,2.5419,0.29853,0.89564,-0.32972,-0.86306,-0.917,0.36494,0.16103,-3.874

> view matrix models
> #4,0.60701,0.25668,0.7521,2.2109,0.31141,0.79388,-0.52228,-1.4919,-0.73114,0.55124,0.40196,-2.9338

> view matrix models
> #4,0.45049,0.81422,0.36621,0.51742,-0.66764,0.57956,-0.46729,-2.0677,-0.59272,-0.033987,0.80469,-1.1867

> view matrix models
> #4,0.4671,0.78438,0.40813,0.68993,-0.53828,0.61845,-0.57252,-2.3398,-0.70148,0.047741,0.71109,-1.6394

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.4671,0.78438,0.40813,6.7112,-0.53828,0.61845,-0.57252,4.5008,-0.70148,0.047741,0.71109,2.9032

> view matrix models
> #4,0.4671,0.78438,0.40813,7.5031,-0.53828,0.61845,-0.57252,3.7516,-0.70148,0.047741,0.71109,4.2369

> view matrix models
> #4,0.4671,0.78438,0.40813,7.0719,-0.53828,0.61845,-0.57252,4.2562,-0.70148,0.047741,0.71109,3.5215

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.49035,0.83805,0.2392,6.4788,-0.5644,0.5145,-0.64555,4.0145,-0.66408,0.18154,0.72529,3.5553

> view matrix models
> #4,-0.082637,0.98267,0.16591,5.6734,-0.86268,0.012818,-0.50559,4.4301,-0.49896,-0.18491,0.84667,4.2574

> select clear

> select add #3

1024 atoms, 1049 bonds, 125 residues, 1 model selected  

> view matrix models
> #3,0.90309,-0.31321,0.29381,-29.512,0.42278,0.76853,-0.48022,-0.70399,-0.075394,0.55791,0.82647,-5.0274

> view matrix models
> #3,0.71463,-0.61043,0.34159,-29.631,0.69949,0.62737,-0.34224,-0.97961,-0.0053901,0.48351,0.87532,-5.1274

> view matrix models
> #3,0.67594,-0.69919,0.23292,-28.876,0.58696,0.31965,-0.74384,1.8238,0.44563,0.6395,0.62645,-3.1868

> view matrix models
> #3,0.74361,-0.66076,0.10218,-28.024,0.62605,0.63444,-0.45337,-0.39694,0.23475,0.4011,0.88544,-4.7414

> view matrix models
> #3,0.73903,-0.61787,0.26848,-29.131,0.56527,0.35194,-0.74606,1.7606,0.36648,0.70312,0.60936,-3.2817

> view matrix models
> #3,0.76438,-0.6045,0.22427,-28.84,0.56538,0.46121,-0.68383,1.2122,0.30994,0.64951,0.69432,-3.8104

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.76438,-0.6045,0.22427,-28.299,0.56538,0.46121,-0.68383,1.6299,0.30994,0.64951,0.69432,-4.2684

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.7391,-0.49912,0.45233,-29.911,0.66745,0.45219,-0.59164,1.2074,0.090753,0.73919,0.66735,-4.5313

> view matrix models
> #3,0.80454,-0.57034,0.1656,-27.928,0.49683,0.49357,-0.71383,1.6759,0.32539,0.65658,0.68046,-4.1711

> view matrix models
> #3,0.68469,-0.72801,-0.034498,-26.612,0.72402,0.68484,-0.082377,-2.2341,0.083598,0.031426,0.996,-5.5535

> view matrix models
> #3,0.83399,-0.44924,0.32037,-29.031,0.50033,0.86052,-0.095796,-2.7138,-0.23265,0.24018,0.94244,-5.9578

> view matrix models
> #3,0.63842,-0.5909,0.49321,-30.169,0.66843,0.74334,0.025354,-3.0681,-0.3816,0.31349,0.86954,-5.8142

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.63842,-0.5909,0.49321,-28.913,0.66843,0.74334,0.025354,-1.6936,-0.3816,0.31349,0.86954,-6.7186

> view matrix models
> #3,0.63842,-0.5909,0.49321,-28.196,0.66843,0.74334,0.025354,-0.023998,-0.3816,0.31349,0.86954,-5.0732

> select clear

> select #4/A:149

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select add #4

1193 atoms, 1216 bonds, 149 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:1

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A

2290 atoms, 2339 bonds, 283 residues, 1 model selected  

> select add #1

2290 atoms, 2339 bonds, 283 residues, 3 models selected  

> select subtract #1

2290 atoms, 2339 bonds, 283 residues, 1 model selected  

> select subtract #2

Nothing selected  

> show #2 models

> select add #2

2290 atoms, 2339 bonds, 283 residues, 1 model selected  

> view matrix models #2,1,0,0,-76.217,0,1,0,-21.724,0,0,1,-28.261

> view matrix models #2,1,0,0,-76.158,0,1,0,-21.999,0,0,1,-27.971

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.60977,-0.39872,0.68498,-75.939,0.78768,0.40083,-0.46787,-23.202,-0.088011,0.82484,0.55848,-27.426

> view matrix models
> #2,0.99942,0.025362,-0.02292,-76.145,-0.022115,0.99097,0.13226,-21.961,0.026067,-0.13168,0.99095,-28.083

> view matrix models
> #2,0.99936,0.025376,-0.025094,-76.145,-0.021788,0.99072,0.13417,-21.961,0.028266,-0.13353,0.99064,-28.086

> ui tool show "Color Actions"

> set bgColor white

> set bgColor #ffffff00

> set bgColor white

> select clear

> select #2/A:1

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:1-180

1451 atoms, 1482 bonds, 180 residues, 1 model selected  

> select #2/A:1

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:1-125

1023 atoms, 1048 bonds, 125 residues, 1 model selected  

> ui tool show "Color Actions"

> set bgColor hot pink

> set bgColor #ff69b400

> set bgColor white

> set bgColor #ffffff00

> color sel hot pink target c

> ui tool show "Fit in Map"

Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #5, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #6, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  

> fitmap #3 inMap #1 resolution 15

Fit map fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 in map
cluster01_gauss_ave07.map.mrc using 328 points  
correlation = 0.8341, correlation about mean = 0.7539, overlap = 278  
steps = 204, shift = 14.5, angle = 51 degrees  
  
Position of fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 (#6) relative
to cluster01_gauss_ave07.map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90802504 -0.39096120 -0.15046546 67.04981108  
0.26846896 0.81881428 -0.50741264 68.78183753  
0.32158192 0.42034808 0.84846482 46.19234613  
Axis 0.75290551 -0.38308054 0.53514726  
Axis point 0.00000000 12.81743682 167.85962439  
Rotation angle (degrees) 38.03336737  
Shift along axis 48.85289622  
  
Average map value = 5.447 for 1024 atoms, 16 outside contour  

> select add #3

2047 atoms, 2097 bonds, 250 residues, 2 models selected  

> view matrix models
> #2,0.99877,0.035422,-0.034772,-76.11,-0.030655,0.99115,0.12916,-21.627,0.039039,-0.12794,0.99101,-28.484,#3,0.90674,-0.38843,-0.16413,-14.032,0.25884,0.81997,-0.51054,5.6663,0.33289,0.42045,0.84404,-3.9904

> select add #2

3314 atoms, 3388 bonds, 408 residues, 2 models selected  

> select subtract #2

1024 atoms, 1049 bonds, 125 residues, 1 model selected  

> view matrix models
> #3,0.89712,-0.41664,-0.14691,-14.112,0.27346,0.78488,-0.55604,6.0217,0.34698,0.45866,0.81807,-3.8651

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.89712,-0.41664,-0.14691,-23.517,0.27346,0.78488,-0.55604,1.2048,0.34698,0.45866,0.81807,-3.5619

Average map value = 5.446 for 1024 atoms, 31 outside contour  
Correlation = 0.8341, Correlation about mean = 0.6517, Overlap = 278  
  
Average map value = 5.446 for 1024 atoms, 31 outside contour  
Correlation = 0.8341, Correlation about mean = 0.6517, Overlap = 278  
  
Average map value = 5.446 for 1024 atoms, 31 outside contour  
Correlation = 0.8341, Correlation about mean = 0.6517, Overlap = 278  
  
Average map value = 5.446 for 1024 atoms, 31 outside contour  
Correlation = 0.8341, Correlation about mean = 0.6517, Overlap = 278  
  

> fitmap #3 inMap #1 resolution 15 metric correlation

Fit map fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 in map
cluster01_gauss_ave07.map.mrc using 328 points  
correlation = 0.8342, correlation about mean = 0.4543, overlap = 277.8  
steps = 180, shift = 4.33, angle = 100 degrees  
  
Position of fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 (#5) relative
to cluster01_gauss_ave07.map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.26697751 0.66753713 0.69506631 52.00937846  
0.39337014 0.58293831 -0.71094505 66.90735274  
-0.87976300 0.46322468 -0.10695776 48.75269363  
Axis 0.59199439 0.79399946 -0.13822987  
Axis point 33.94424725 0.00000000 26.70168126  
Rotation angle (degrees) 97.38413300  
Shift along axis 77.17458410  
  
Average map value = 5.441 for 1024 atoms, 235 outside contour  

> fitmap #3 inMap #1 resolution 15 metric correlation

Fit map fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 in map
cluster01_gauss_ave07.map.mrc using 328 points  
correlation = 0.8342, correlation about mean = 0.4538, overlap = 277.8  
steps = 40, shift = 0.0281, angle = 0.0499 degrees  
  
Position of fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 (#5) relative
to cluster01_gauss_ave07.map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.26717044 0.66739415 0.69512949 52.00526758  
0.39411773 0.58258656 -0.71081932 66.92713298  
-0.87936976 0.46387277 -0.10738196 48.77306881  
Axis 0.59228035 0.79386332 -0.13778611  
Axis point 33.90958811 0.00000000 26.72321353  
Rotation angle (degrees) 97.40097545  
Shift along axis 77.21244290  
  
Average map value = 5.441 for 1024 atoms, 236 outside contour  
[Repeated 1 time(s)]Correlation = 0.8342, Correlation about mean = 0.4538,
Overlap = 277.8  
  

> fitmap #3 inMap #1 resolution 15

Fit map fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 in map
cluster01_gauss_ave07.map.mrc using 328 points  
correlation = 0.8341, correlation about mean = 0.7541, overlap = 278  
steps = 276, shift = 13.2, angle = 100 degrees  
  
Position of fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 (#5) relative
to cluster01_gauss_ave07.map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90839483 -0.38971863 -0.15145366 67.13055429  
0.26225011 0.81319198 -0.51956105 68.79914893  
0.32564352 0.43224784 0.84090315 46.18745414  
Axis 0.76239304 -0.38215189 0.52222293  
Axis point 0.00000000 12.68364068 163.90442138  
Rotation angle (degrees) 38.62529362  
Shift along axis 49.00828993  
  
Average map value = 5.447 for 1024 atoms, 16 outside contour  

> view matrix models
> #3,0.90839,-0.38972,-0.15145,-25.744,0.26225,0.81319,-0.51956,-0.040249,0.32564,0.43225,0.8409,-3.1573

> view matrix models
> #3,0.90839,-0.38972,-0.15145,-25.359,0.26225,0.81319,-0.51956,0.41952,0.32564,0.43225,0.8409,-3.7765

> view matrix models
> #3,0.90839,-0.38972,-0.15145,-24.392,0.26225,0.81319,-0.51956,0.86429,0.32564,0.43225,0.8409,-3.8944

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.92801,-0.37249,-0.0066323,-25.294,0.21143,0.54123,-0.81386,3.03,0.30675,0.75387,0.58102,-2.7705

> view matrix models
> #3,0.91163,-0.19269,0.36304,-27.887,0.40193,0.6026,-0.68944,2.4241,-0.085922,0.77443,0.6268,-3.6231

> view matrix models
> #3,0.97045,-0.16927,0.172,-26.648,0.22194,0.90587,-0.36076,-0.31762,-0.094747,0.38827,0.91666,-4.8773

> view matrix models
> #3,0.94323,-0.30867,0.12265,-26.173,0.33214,0.87882,-0.34258,-0.24071,-0.0020417,0.36387,0.93145,-4.807

> view matrix models
> #3,0.81097,-0.52252,0.26326,-26.918,0.55094,0.83344,-0.042942,-1.7446,-0.19698,0.17987,0.96377,-5.0052

> view matrix models
> #3,0.80384,-0.51824,0.29201,-27.113,0.57018,0.81117,-0.12998,-1.1425,-0.1695,0.27098,0.94754,-5.0001

> view matrix models
> #3,0.80642,-0.53603,0.24972,-26.82,0.56389,0.82423,-0.051733,-1.6585,-0.17809,0.18253,0.96694,-5.0031

> view matrix models
> #3,0.61793,-0.68377,0.3881,-27.724,0.71765,0.69215,0.076808,-2.0566,-0.32114,0.23106,0.91841,-4.9671

> select subtract #3

Nothing selected  

> select add #3

1024 atoms, 1049 bonds, 125 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #4

1193 atoms, 1216 bonds, 149 residues, 1 model selected  

> view matrix models
> #4,-0.37197,0.22205,-0.90129,1.9472,0.23408,0.96203,0.1404,7.3056,0.89824,-0.15875,-0.40982,1.0395

> view matrix models
> #4,-0.41205,0.24644,-0.8772,1.9884,0.21068,0.96241,0.17142,7.3942,0.88647,-0.11417,-0.44848,0.87725

> view matrix models
> #4,-0.41872,0.34663,-0.83936,2.0794,0.34716,0.91518,0.20475,7.6465,0.83913,-0.20566,-0.50354,0.67589

Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #7, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #8, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  

> fitmap #4 inMap #1 resolution 15

Fit map fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 in map
cluster01_gauss_ave07.map.mrc using 358 points  
correlation = 0.8487, correlation about mean = 0.7254, overlap = 324.5  
steps = 116, shift = 18.8, angle = 43.7 degrees  
  
Position of fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 (#8) relative
to cluster01_gauss_ave07.map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.28859660 -0.24862676 -0.92460626 64.31479429  
0.53669347 0.75770837 -0.37126559 68.94613354  
0.79288846 -0.60337613 -0.08523570 48.45026337  
Axis -0.12198800 -0.90264640 0.41273284  
Axis point -0.34867559 0.00000000 63.43740363  
Rotation angle (degrees) 107.94247444  
Shift along axis -50.08259760  
  
Average map value = 5.446 for 1193 atoms, 19 outside contour  

> view matrix models
> #4,-0.27314,-0.24278,-0.93084,-16.79,0.53666,0.7646,-0.3569,6.2127,0.79837,-0.59703,-0.078551,-2.1338

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.27314,-0.24278,-0.93084,-1.6204,0.53666,0.7646,-0.3569,13.792,0.79837,-0.59703,-0.078551,5.7757

> view matrix models
> #4,-0.27314,-0.24278,-0.93084,-2.6703,0.53666,0.7646,-0.3569,13.094,0.79837,-0.59703,-0.078551,5.6964

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.54665,0.11316,-0.82968,-2.68,0.36347,0.92468,-0.11336,13.742,0.75436,-0.36353,-0.54661,3.9286

> view matrix models
> #4,-0.54119,0.087788,-0.83631,-2.6894,0.34291,0.93113,-0.12416,13.684,0.76781,-0.35397,-0.53402,3.9811

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.54119,0.087788,-0.83631,0.82188,0.34291,0.93113,-0.12416,11.548,0.76781,-0.35397,-0.53402,1.02

> view matrix models
> #4,-0.54119,0.087788,-0.83631,0.72888,0.34291,0.93113,-0.12416,11.566,0.76781,-0.35397,-0.53402,1.0488

> view matrix models
> #4,-0.54119,0.087788,-0.83631,1.2465,0.34291,0.93113,-0.12416,9.1435,0.76781,-0.35397,-0.53402,2.644

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.62753,0.037508,-0.77769,1.3961,0.3006,0.93306,-0.19756,8.8482,0.71822,-0.35775,-0.5968,2.3818

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.62753,0.037508,-0.77769,-0.31486,0.3006,0.93306,-0.19756,9.5763,0.71822,-0.35775,-0.5968,2.8785

> view matrix models
> #4,-0.62753,0.037508,-0.77769,-0.44311,0.3006,0.93306,-0.19756,9.2402,0.71822,-0.35775,-0.5968,3.6067

> select clear

> select #1

2 models selected  

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> select clear

> lighting full

> lighting flat

> save
> /Users/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/fitting_cluster01_gauss_ave07.cxs

——— End of log from Fri Feb 6 16:10:03 2026 ———

opened ChimeraX session  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #2 models

> hide #3 models

> show #3 models

> volume #1 level 5.436

> volume #1 level 5.437

> ui tool show "Fit in Map"

Average map value = 5.444 for 1024 atoms, 94 outside contour  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #9, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 15 as #10, grid size
28,25,26, pixel 5, shown at level 0.0266, step 1, values float32  
Correlation = 0.8341, Correlation about mean = 0.6223, Overlap = 277.9  
  
Average map value = 5.444 for 1024 atoms, 94 outside contour  
Correlation = 0.8341, Correlation about mean = 0.6223, Overlap = 277.9  
  
Average map value = 5.444 for 1024 atoms, 94 outside contour  
Correlation = 0.8341, Correlation about mean = 0.6223, Overlap = 277.9  
  
Average map value = 5.444 for 1024 atoms, 94 outside contour  
Correlation = 0.8341, Correlation about mean = 0.6223, Overlap = 277.9  
  
Average map value = 5.443 for 1193 atoms, 90 outside contour  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #11, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 as #12, grid size
25,27,28, pixel 5, shown at level 0.0308, step 1, values float32  
Correlation = 0.8487, Correlation about mean = 0.6077, Overlap = 324.4  
  

> volume #1 level 5.442

Average map value = 5.443 for 1193 atoms, 445 outside contour  
Correlation = 0.8487, Correlation about mean = 0.6077, Overlap = 324.4  
  
Average map value = 5.443 for 1193 atoms, 445 outside contour  
Correlation = 0.8487, Correlation about mean = 0.6077, Overlap = 324.4  
  
Average map value = 5.443 for 1193 atoms, 445 outside contour  
Correlation = 0.8487, Correlation about mean = 0.6077, Overlap = 324.4  
  

> volume #1 level 5.437

> fitmap #4 inMap #1 resolution 15 metric correlation

Fit map fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 in map
cluster01_gauss_ave07.map.mrc using 358 points  
correlation = 0.8488, correlation about mean = 0.4666, overlap = 324  
steps = 228, shift = 7.98, angle = 94.2 degrees  
  
Position of fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 15 (#11)
relative to cluster01_gauss_ave07.map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69271416 0.56660220 0.44621635 85.16228556  
0.06699721 0.66658275 -0.74241417 64.17328332  
-0.71809363 -0.48438556 -0.49971208 55.08733782  
Axis 0.19956092 0.90048451 -0.38639758  
Axis point 50.89625078 0.00000000 26.14500606  
Rotation angle (degrees) 139.72245412  
Shift along axis 53.49649724  
  
Average map value = 5.438 for 1193 atoms, 470 outside contour  
[Repeated 1 time(s)]Correlation = 0.8488, Correlation about mean = 0.4666,
Overlap = 324  
  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 as #11, grid size
28,31,33, pixel 3.33, shown at level 0.0494, step 1, values float32  

> fitmap #4 inMap #1 resolution 10 metric correlation

Fit map fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 in map
cluster01_gauss_ave07.map.mrc using 896 points  
correlation = 0.8912, correlation about mean = 0.482, overlap = 1094  
steps = 136, shift = 9.48, angle = 74.2 degrees  
  
Position of fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 (#11)
relative to cluster01_gauss_ave07.map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96557807 -0.23850226 0.10380585 87.84268205  
-0.18640429 0.91280931 0.36336291 65.26730169  
-0.18141782 0.33150540 -0.92584650 52.02536669  
Axis -0.10921791 0.97783963 0.17860883  
Axis point 49.09130241 0.00000000 16.49884790  
Rotation angle (degrees) 171.61385600  
Shift along axis 63.51914982  
  
Average map value = 5.44 for 1193 atoms, 404 outside contour  
[Repeated 1 time(s)]Correlation = 0.8912, Correlation about mean = 0.482,
Overlap = 1094  
  

> select add #3

1024 atoms, 1049 bonds, 125 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.61793,-0.68377,0.3881,-27.083,0.71765,0.69215,0.076808,-1.0611,-0.32114,0.23106,0.91841,-5.5741

Average map value = 5.445 for 1024 atoms, 86 outside contour  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #9, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #10, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Correlation = 0.8828, Correlation about mean = 0.4984, Overlap = 938.4  
  
Average map value = 5.445 for 1024 atoms, 86 outside contour  
Correlation = 0.8828, Correlation about mean = 0.4984, Overlap = 938.4  
  
Average map value = 5.445 for 1024 atoms, 86 outside contour  
Correlation = 0.8828, Correlation about mean = 0.4984, Overlap = 938.4  
  
Average map value = 5.445 for 1024 atoms, 86 outside contour  
Correlation = 0.8828, Correlation about mean = 0.4984, Overlap = 938.4  
  

> fitmap #3 inMap #1 resolution 10 metric cam

Fit map fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 in map
cluster01_gauss_ave07.map.mrc using 792 points  
correlation = 0.8828, correlation about mean = 0.6428, overlap = 938.7  
steps = 120, shift = 7.41, angle = 37 degrees  
  
Position of fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 (#9) relative
to cluster01_gauss_ave07.map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.87744038 -0.42316327 0.22590092 59.25930981  
0.47696247 0.71954536 -0.50473882 67.81834154  
0.05104097 0.55062448 0.83319115 44.99065712  
Axis 0.75487267 0.12507256 0.64383546  
Axis point 0.00000000 41.87254785 90.73261704  
Rotation angle (degrees) 44.34955182  
Shift along axis 82.18202796  
  
Average map value = 5.447 for 1024 atoms, 40 outside contour  

> view matrix models
> #3,0.87744,-0.42316,0.2259,-27.651,0.47696,0.71955,-0.50474,1.173,0.051041,0.55062,0.83319,-5.366

> view matrix models
> #3,0.87744,-0.42316,0.2259,-27.605,0.47696,0.71955,-0.50474,1.0869,0.051041,0.55062,0.83319,-5.2498

> volume #1 level 5.438

Average map value = 5.445 for 1024 atoms, 79 outside contour  
Correlation = 0.8828, Correlation about mean = 0.5659, Overlap = 938.5  
  
Average map value = 5.445 for 1024 atoms, 79 outside contour  
Correlation = 0.8828, Correlation about mean = 0.5659, Overlap = 938.5  
  
Average map value = 5.445 for 1024 atoms, 79 outside contour  
Correlation = 0.8828, Correlation about mean = 0.5659, Overlap = 938.5  
  
Average map value = 5.445 for 1024 atoms, 79 outside contour  
Correlation = 0.8828, Correlation about mean = 0.5659, Overlap = 938.5  
  
Average map value = 5.445 for 1024 atoms, 79 outside contour  
Correlation = 0.8828, Correlation about mean = 0.5659, Overlap = 938.5  
  

> view matrix models
> #3,0.87744,-0.42316,0.2259,-25.772,0.47696,0.71955,-0.50474,2.577,0.051041,0.55062,0.83319,-5.5878

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.80889,-0.43945,0.39061,-26.87,0.57871,0.71241,-0.39695,2.0539,-0.10384,0.54714,0.83058,-5.7781

> save
> /Users/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/fitting_cluster01_gauss_ave07.cxs

——— End of log from Fri Feb 6 16:30:53 2026 ———

opened ChimeraX session  

> ui tool show "Fit in Map"

Average map value = 5.412 for 1355 atoms, 2290 outside contour  
Opened fold_2025_05_19_synaptotagmin_140_422_model_0.cif map 10 as #12, grid
size 38,33,35, pixel 3.33, shown at level 0.0583, step 1, values float32  
Opened fold_2025_05_19_synaptotagmin_140_422_model_0.cif map 10 as #13, grid
size 38,33,35, pixel 3.33, shown at level 0.0583, step 1, values float32  
Correlation = 0.702, Correlation about mean = 0.00228, Overlap = 1255  
  
Average map value = 5.446 for 1024 atoms, 65 outside contour  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #14, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Opened fold_2025_08_07_syanptotagmin_c2a_model_0.cif map 10 as #15, grid size
33,28,29, pixel 3.33, shown at level 0.0458, step 1, values float32  
Correlation = 0.8828, Correlation about mean = 0.6012, Overlap = 938.5  
  
Average map value = 5.443 for 1193 atoms, 136 outside contour  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 as #16, grid size
28,31,33, pixel 3.33, shown at level 0.0494, step 1, values float32  
Opened fold_2025_08_07_synaptotagmin_c2b_model_0.cif map 10 as #17, grid size
28,31,33, pixel 3.33, shown at level 0.0494, step 1, values float32  
Correlation = 0.8911, Correlation about mean = 0.5004, Overlap = 1095  
  

> select clear

> save
> /Volumes/PegasusP32T_H29_04/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/cluster01_gauss_ave07.cxs

——— End of log from Thu Feb 12 15:20:18 2026 ———

opened ChimeraX session  

> ui tool show "Hide Dust"

> surface dust #1 size 10.51

> select #3/A:1

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 2 residues  

> cartoon hide sel

> volume #1 level 5.433

> save
> /Volumes/PegasusP32T_H29_04/rina/Unix/synaptotagmin/to_rina.dec12-2024/0mMCa-10/rec-05-10sets/clusters-2024:04:16:17:27/cluster01/avemaps/cluster01_gauss_ave07.cxs

> volume zone #map near #model1 distance 4

Missing or invalid "volumes" argument: invalid density maps specifier  

> volume zone #map near #model1 distance 4

Missing or invalid "volumes" argument: invalid density maps specifier  

> close #5-17

> volume zone #1 nearAtoms #3 distance 4

Expected a keyword  

> volume zone #1 nearAtoms #3 distance

Expected a keyword  

> watershed #1

Unknown command: segmentation watershed #1  

>

Unknown command: segmentation #1  

> select #1

2 models selected  

> ui tool show "Segment Map"

Segmenting cluster01_gauss_ave07.map.mrc, density threshold 5.433286  
Showing 1 region surfaces  
37 watershed regions, grouped to 1 regions  
Showing cluster01_gauss_ave07.map.seg - 1 regions, 1 surfaces  
Ungrouped to 3 regions  

> hide #5.4 models

> show #5.4 models

> hide #5.3 models

> show #5.3 models

> hide #5.3 models

> show #5.3 models

> hide #5.2 models

> show #5.2 models

> hide #5.2 models

> show #5.2 models

> hide #5.2 models

> show #5.2 models

> close #5.3

> hide #5.2 models

> show #5.2 models

Smoothing and grouping, standard deviation 3 voxels  
Showing 1 region surfaces  
Got 1 regions after smoothing 3 voxels.  

> hide #!5 models

> show #!5 models

> hide #5.1 models

> show #5.1 models

Ungrouped to 3 regions  

> hide #5.3 models

> show #5.3 models

Segmenting cluster01_gauss_ave07.map.mrc, density threshold 5.433286  
Showing 34 region surfaces  
37 watershed regions, grouped to 34 regions  
Showing cluster01_gauss_ave07.map.seg - 34 regions, 34 surfaces  

> select subtract #1

Nothing selected  

> select add #5

35 models selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,-0.25238,0,1,0,2.201,0,0,1,-3.3339

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.80112,-0.38217,0.46061,-7.5087,0.29178,0.92132,0.25696,-27.235,-0.52257,-0.071458,0.8496,36.072

> view matrix models
> #5,0.8328,-0.40345,0.37904,-2.4763,0.23756,0.87893,0.41359,-34.098,-0.50001,-0.25439,0.82781,43.323

> view matrix models
> #5,0.93611,0.21524,0.27817,-23.77,0.10955,-0.92997,0.35092,40.755,0.33422,-0.29803,-0.89413,103.38

> view matrix models
> #5,0.9898,0.10969,0.090959,-18.835,-0.068776,0.92679,-0.36924,16.856,-0.1248,0.35922,0.92487,-6.0833

> hide #!1 models

> hide #3 models

> hide #4 models

> surface dust #1 size 10.51

[Repeated 2 time(s)]

> select add #1

37 models selected  

> show #!1 models

> hide #!1 models

> select subtract #1

35 models selected  

> close #5

> show #!1 models

> select #1

2 models selected  

> ui tool show "Segment Map"

Segmenting cluster01_gauss_ave07.map.mrc, density threshold 5.433286  
Showing 1 region surfaces  
37 watershed regions, grouped to 1 regions  
Showing cluster01_gauss_ave07.map.seg - 1 regions, 1 surfaces  
Ungrouped to 3 regions  
Ungrouped to 12 regions  
Ungrouped to 34 regions  
Ungrouped to 0 regions  
[Repeated 1 time(s)]Got 35 regions after grouping by connections  
Got 34 regions after grouping by connections  
Got 33 regions after grouping by connections  
Ungrouped to 2 regions  
[Repeated 1 time(s)]Ungrouped to 4 regions  
Got 35 regions after grouping by connections  
Segmenting cluster01_gauss_ave07.map.mrc, density threshold 5.433286  
Showing 34 region surfaces  
37 watershed regions, grouped to 34 regions  
Showing cluster01_gauss_ave07.map.seg - 34 regions, 34 surfaces  
Ungrouped to 2 regions  
Smoothing and grouping, standard deviation 1 voxels  
Showing 12 region surfaces  
Got 12 regions after smoothing 1 voxels.  

> select #1

2 models selected  

> select #1

2 models selected  

> select clear

> select #5.1

1 model selected  

> select #5.2

1 model selected  

> select #5.1

1 model selected  

> select clear

> hide #!1 models

Drag select of 17, 5, 43, 224 of 15168 triangles, 46, 194 of 292 triangles,
45, 44, 41, 42, 100 of 148 triangles, 49, 110 of 128 triangles, 47  

> select clear

Drag select of 17, 37, 5, 43, 224 of 15168 triangles, 46, 45, 44, 41, 42, 49,
47  

> select clear

> select #5.1

1 model selected  

> select #5.2

1 model selected  

> select #5.1

1 model selected  

> select clear

> select #5.1

1 model selected  

> select #5.2

1 model selected  

> select #5.1

1 model selected  

> select clear

> select #5.1

1 model selected  

> measure center #5

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro Vega 64 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac Pro
      Model Identifier: iMacPro1,1
      Processor Name: 18-Core Intel Xeon W
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 18
      L2 Cache (per Core): 1 MB
      L3 Cache: 24.8 MB
      Hyper-Threading Technology: Enabled
      Memory: 128 GB
      System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
      OS Loader Version: 582~3311

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 135 days, 19 minutes

Graphics/Displays:

    Radeon Pro Vega 64:

      Chipset Model: Radeon Pro Vega 64
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 16 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6860
      Revision ID: 0x0000
      ROM Revision: 113-D0500D-114
      VBIOS Version: 113-D05001A1XT-018
      Option ROM Version: 113-D05001A1XT-018
      EFI Driver Version: 01.01.114
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Thunderbolt Display:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: C02M44S1F2GC
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    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: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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
    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: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Eric Pettersen]

I think model #5 was a segmentation

[Tom Goddard]

This was fixed in May 2025. Use current ChimeraX 1.11 to avoid this bug.

The problem is measuring the center that involves empty surfaces. The fixed code properly handles that.