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Opened 5 hours ago
#19861 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
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
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