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Opened 7 months ago
Closed 7 months ago
#17173 closed defect (fixed)
volume gaussian: update histogram: cannot convert float NaN to integer
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.2-arm64-arm-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:
Startup Messages
---
note | available bundle cache has not been initialized yet
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 /Users/sahtelis/Downloads/cryosparc_P7_J67_004_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc as #1, grid size 192,192,192,
pixel 1.84, shown at level 0.319, step 1, values float32
> volume #1 level 2.458
> surface dust #1 size 18.4
> volume #1 level 1.58
[Repeated 1 time(s)]
> volume #1 level 1.287
> volume #1 level 1.647
> volume #1 level 1.152
> volume #1 level 1.175
> volume #1 level 1.355
> volume #1 level 1.602
> hide #!1 models
> show #!1 models
> open /Users/sahtelis/Downloads/cryosparc_P7_J170_class_00_final_volume.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J170_class_01_final_volume.mrc
Opened cryosparc_P7_J170_class_00_final_volume.mrc as #2.1, grid size
256,256,256, pixel 1.38, shown at level 0.228, step 1, values float32
Opened cryosparc_P7_J170_class_01_final_volume.mrc as #2.2, grid size
256,256,256, pixel 1.38, shown at level 0.266, step 1, values float32
> surface dust #1 size 18.4
> surface dust #2.1 size 13.8
> surface dust #2.2 size 13.8
> hide #!1 models
> volume #2.1 level 0.542
> hide #!2.2 models
> volume #2.1 level 0.6937
> show #!2.2 models
> hide #!2.1 models
> volume #2.2 level 0.5322
> volume #2.2 level 0.8373
> volume #2.2 level 0.8329
> surface dust #2.2 size 13.8
> volume #2.2 level 0.5584
> open /Users/sahtelis/Downloads/cryosparc_P7_J171_004_volume_map_sharp.mrc
Opened cryosparc_P7_J171_004_volume_map_sharp.mrc as #3, grid size
384,384,384, pixel 0.92, shown at level 0.111, step 2, values float32
> volume #3 level 0.3626
> hide #!2.2 models
> volume #3 level 0.7304
> surface dust #3 size 9.2
> volume #3 level 0.5078
> volume #3 level 0.6142
> volume #3 level 0.7207
> volume #3 level 0.7401
> show #!1 models
> tile
2 models tiled
> volume #3 level 0.5465
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.012478,-0.50749,0.86157,82.155,-0.49977,0.74946,0.43421,141.99,-0.86607,-0.42517,-0.26298,429.54
> view matrix models
> #3,-0.64302,-0.73195,-0.22533,421.95,-0.74469,0.66626,-0.039146,282.16,0.17878,0.14263,-0.97349,268.08
> select subtract #3
Nothing selected
> select add #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91281,-0.39256,0.11255,19.954,0.36248,0.90579,0.21944,12.912,-0.18809,-0.15951,0.96911,47.529
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.8147,-0.54464,0.19906,49.124,0.51119,0.83662,0.19686,2.7828,-0.27376,-0.058628,0.96001,46.421
> select subtract #3
Nothing selected
> volume #3 level 0.6142
> volume #1 level 1.672
> volume #1 color #bf8b4a
> volume #1 color #bf7422
> volume #1 color #bf945d
> set bgColor gray
> transparency #1,3#!2 0
> volume #3 level 0.6917
> hide #!3 models
> hide #!2 models
> volume #1 level 1.672
> volume #1 level 1.62
> open /Users/sahtelis/Desktop/cx43_hc.pdb
Chain information for cx43_hc.pdb #4
---
Chain | Description
A B C D E F | No description available
> volume #1 level 1.527
> volume #1 level 1.69
> open /Users/sahtelis/Downloads/cryosparc_P7_J174_mask.mrc
Opened cryosparc_P7_J174_mask.mrc as #5, grid size 192,192,192, pixel 1.84,
shown at level 0.168, step 1, values float32
> volume #5 level 0.09218
> volume #5 level 0.1975
> open /Users/sahtelis/Downloads/cryosparc_P7_J175_mask.mrc
Opened cryosparc_P7_J175_mask.mrc as #6, grid size 192,192,192, pixel 1.84,
shown at level 0.399, step 1, values float32
> hide #!5 models
> volume #6 level 0.2311
> volume #6 level 0.5989
> volume #1 level 1.759
> hide #!6 models
> hide #!4 models
> volume #1 level 1.62
> volume #1 level 1.597
> volume #1 level 1.736
> volume #1 level 2.014
> open /Users/sahtelis/Downloads/cryosparc_P7_J176_mask.mrc
Opened cryosparc_P7_J176_mask.mrc as #7, grid size 192,192,192, pixel 1.84,
shown at level 0.658, step 1, values float32
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> open /Users/sahtelis/Downloads/cryosparc_P7_J177_mask.mrc
Opened cryosparc_P7_J177_mask.mrc as #8, grid size 192,192,192, pixel 1.84,
shown at level 5e-05, step 1, values float32
> hide #!6 models
> volume #8 level 0.7154
> hide #!1 models
> volume #8 level 0.1904
> volume #8 level 0.562
> open /Users/sahtelis/Downloads/cryosparc_P7_J172_mask.mrc
Opened cryosparc_P7_J172_mask.mrc as #9, grid size 192,192,192, pixel 1.84,
shown at level 0.31, step 1, values float32
> hide #!8 models
> volume #9 level 0.7188
> volume #9 level 0.8131
> volume #9 level 0.9535
> volume #9 level 0.7631
> volume #9 level 0.7853
> open /Users/sahtelis/Downloads/cryosparc_P7_J179_mask.mrc
Opened cryosparc_P7_J179_mask.mrc as #10, grid size 192,192,192, pixel 1.84,
shown at level 0.00115, step 1, values float32
> volume #10 level 0.1435
> hide #!9 models
> volume #10 level 0.661
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!9 models
> open /Users/sahtelis/Downloads/cryosparc_P7_J180_mask.mrc
Opened cryosparc_P7_J180_mask.mrc as #11, grid size 192,192,192, pixel 1.84,
shown at level 5e-05, step 1, values float32
> hide #!9 models
> volume #11 level 0.2126
> show #!9 models
> hide #!11 models
> open /Users/sahtelis/Downloads/cryosparc_P7_J181_005_volume_map_sharp.mrc
Opened cryosparc_P7_J181_005_volume_map_sharp.mrc as #12, grid size
192,192,192, pixel 1.84, shown at level 0.29, step 1, values float32
> close #10
> close #11
> close #8
> close #7
> close #6
> close #5
> volume #12 level 1.695
> surface dust #9 size 18.4
> surface dust #12 size 18.4
> hide #!9 models
> volume #12 level 2.574
> volume #12 level 1.344
> volume #12 level 1.783
> volume #12 level 1.827
> volume #12 level 1.651
> show #!3 models
> hide #!12 models
> hide #!3 models
> show #!2 models
> close #2
> show #!1 models
> volume #1 level 1.62
> hide #!1 models
> hide #!9 models
> show #!12 models
> hide #!12 models
> open /Users/sahtelis/Downloads/cryosparc_P7_J184_mask.mrc
Opened cryosparc_P7_J184_mask.mrc as #2, grid size 192,192,192, pixel 1.84,
shown at level 0.132, step 1, values float32
> show #!1 models
> tile
2 models tiled
> volume #1 level 1.5
> volume #1 level 1.6
> volume #1 level 1.75
> close #2
> volume #1 level 1.611
> open /Users/sahtelis/Downloads/cryosparc_P7_J184_mask.mrc
Opened cryosparc_P7_J184_mask.mrc as #2, grid size 192,192,192, pixel 1.84,
shown at level 0.132, step 1, values float32
> close #2
> open /Users/sahtelis/Downloads/cryosparc_P7_J186_mask.mrc
Opened cryosparc_P7_J186_mask.mrc as #2, grid size 192,192,192, pixel 1.84,
shown at level 0.179, step 1, values float32
> volume #2 level 0.695
> hide #!1 models
> show #!9 models
> tile
2 models tiled
> volume #2 level 0.2458
> volume #9 level 0.2437
> show #!12 models
> hide #!9 models
> hide #!2 models
> select add #12
2 models selected
> view matrix models
> #12,0.40599,-0.51004,0.75831,72.746,-0.43251,-0.83819,-0.33222,454.45,0.80505,-0.1931,-0.56089,144.02
> select subtract #12
Nothing selected
> volume #12 level 1.783
> volume #12 level 1.651
> volume #12 level 1.959
> volume #12 level 3.803
> volume #12 level 4.067
> volume #12 level 3.013
> volume #12 level 2.442
> open /Users/sahtelis/Downloads/cryosparc_P7_J182_003_volume_map_sharp.mrc
Opened cryosparc_P7_J182_003_volume_map_sharp.mrc as #5, grid size
192,192,192, pixel 1.84, shown at level 0.298, step 1, values float32
> volume #5 level 1.138
> surface dust #12 size 18.4
> surface dust #5 size 18.4
> hide #!12 models
> volume #5 level 2.472
> volume #5 level 1.261
> volume #5 level 2.348
> volume #5 level 0.8662
> volume #5 level 1.533
> volume #5 level 2.669
> volume #5 level 1.904
> volume #5 level 0.8909
> volume #5 level 1.064
> hide #!5 models
> open /Users/sahtelis/Downloads/cryosparc_P7_J187_003_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J188_003_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J189_002_volume_map_sharp.mrc
Opened cryosparc_P7_J187_003_volume_map_sharp.mrc as #6.1, grid size
192,192,192, pixel 1.84, shown at level 0.238, step 1, values float32
Opened cryosparc_P7_J188_003_volume_map_sharp.mrc as #6.2, grid size
192,192,192, pixel 1.84, shown at level 0.249, step 1, values float32
Opened cryosparc_P7_J189_002_volume_map_sharp.mrc as #6.3, grid size
192,192,192, pixel 1.84, shown at level 0.411, step 1, values float32
> surface dust #6.1 size 18.4
> surface dust #6.2 size 18.4
> surface dust #6.3 size 18.4
> hide #!6.2 models
> hide #!6.3 models
> volume #6.1 level 1.538
> volume #6.1 level 1.592
> hide #!6.1 models
> show #!6.2 models
> volume #6.2 level 1.855
> volume #6.3 level 2.655
> hide #!6.2 models
> volume #6.3 level 1.467
> close #6.3
> show #!6.2 models
> show #!6.1 models
> tile
2 models tiled
> volume #6.1 level 1.701
> hide #!6.2 models
> show #!1 models
> tile
2 models tiled
> show #!5 models
> hide #!5 models
> open /Users/sahtelis/Downloads/cryosparc_P7_J181_005_volume_map_sharp.mrc
Opened cryosparc_P7_J181_005_volume_map_sharp.mrc as #7, grid size
192,192,192, pixel 1.84, shown at level 0.29, step 1, values float32
> volume #7 level 1.959
> surface dust #1 size 18.4
> surface dust #6.1 size 18.4
> surface dust #7 size 18.4
> hide #!6 models
> hide #!1 models
> volume #7 level 2.047
> volume #7 level 2.266
> volume #7 level 1.739
> show #!1 models
> tile
2 models tiled
> hide #!6.1 models
> hide #!7 models
> volume #1 level 1.611
> transparency #1 50
> volume #1 level 1.63
> volume #1 level 1.65
> volume #1 level 1.67
> volume #1 level 1.7
> close #2-3,5-7,9,12
> show #!4 models
> hide atoms
> show cartoons
Computing secondary structure
> select add #4
10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected
> view matrix models
> #4,-0.018846,-0.4657,-0.88474,286.27,0.92731,-0.339,0.15868,40.128,-0.37382,-0.81744,0.43823,215.32
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.018846,-0.4657,-0.88474,303.04,0.92731,-0.339,0.15868,49.652,-0.37382,-0.81744,0.43823,251.66
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.84735,-0.0029801,-0.53102,89.998,0.28511,-0.84108,0.45967,175.51,-0.448,-0.5409,-0.71185,333.7
> view matrix models
> #4,0.70811,-0.2339,0.66624,26.121,0.12191,-0.88888,-0.44163,289.7,0.6955,0.39394,-0.6009,42.576
> view matrix models
> #4,0.24677,-0.39361,0.88554,89.109,0.46426,-0.75409,-0.46455,227.47,0.85063,0.52576,-0.0033529,-52.983
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.24677,-0.39361,0.88554,115.44,0.46426,-0.75409,-0.46455,257.59,0.85063,0.52576,-0.0033529,-26.552
> ui tool show "Fit in Map"
> fitmap #4 inMap #1
Fit molecule cx43_hc.pdb (#4) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#1) using 10620 atoms
average map value = 0.7048, steps = 96
shifted from previous position = 5.78
rotated from previous position = 16.8 degrees
atoms outside contour = 9189, contour level = 1.7
Position of cx43_hc.pdb (#4) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.17767240 -0.98408959 0.00046716 285.47144402
0.98408967 0.17767249 0.00018377 19.80463335
-0.00026385 0.00042707 0.99999988 67.67121995
Axis 0.00012362 0.00037141 0.99999992
Axis point 130.89636147 180.69836890 0.00000000
Rotation angle (degrees) 79.76578809
Shift along axis 67.71385961
> transparency (#!4 & sel) 0
> select subtract #4
Nothing selected
> hide #!4 models
> show #!4 models
> transparency 50
> select add #4
10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.2225,-0.081701,0.9715,64.65,0.58851,-0.7832,-0.20065,222.15,0.77727,0.61638,-0.12618,-13.505
> view matrix models
> #4,0.13086,-0.10151,0.98619,78.299,0.60977,-0.77609,-0.16079,214.53,0.7817,0.6224,-0.039664,-23.141
> view matrix models
> #4,0.22135,0.0078136,0.97516,52.373,0.79165,-0.58538,-0.175,165.58,0.56948,0.81072,-0.13576,-10.778
> fitmap #4 inMap #1
Fit molecule cx43_hc.pdb (#4) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#1) using 10620 atoms
average map value = 0.961, steps = 76
shifted from previous position = 1.49
rotated from previous position = 11.8 degrees
atoms outside contour = 8494, contour level = 1.7
Position of cx43_hc.pdb (#4) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.56201230 -0.82712888 -0.00004343 212.40678937
0.82712885 0.56201226 0.00033896 -10.92352773
-0.00025596 -0.00022642 0.99999995 66.27217805
Axis -0.00034177 0.00012847 0.99999993
Axis point 116.53715517 195.11780892 0.00000000
Rotation angle (degrees) 55.80492731
Shift along axis 66.19817568
> select subtract #4
Nothing selected
> volume #1 level 1.6
> volume #1 level 1.62
> select /C
1771 atoms, 1780 bonds, 1 pseudobond, 230 residues, 2 models selected
> select /D
1770 atoms, 1780 bonds, 1 pseudobond, 229 residues, 2 models selected
> color (#!4 & sel) cyan
> select /F
1771 atoms, 1780 bonds, 1 pseudobond, 230 residues, 2 models selected
> color (#!4 & sel) light sea green
> select add #4
10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> show #!4 models
> select /F
1771 atoms, 1780 bonds, 1 pseudobond, 230 residues, 2 models selected
> color (#!4 & sel) medium blue
> select add #4
10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected
> select subtract #4
Nothing selected
> select /F
1771 atoms, 1780 bonds, 1 pseudobond, 230 residues, 2 models selected
> color (#!4 & sel) lime
> select add #4
10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected
> select subtract #4
Nothing selected
> select /B
1769 atoms, 1780 bonds, 1 pseudobond, 228 residues, 2 models selected
> select /C
1771 atoms, 1780 bonds, 1 pseudobond, 230 residues, 2 models selected
> color (#!4 & sel) yellow
> select add #4
10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected
> select subtract #4
Nothing selected
> open /Users/sahtelis/Desktop/cx45_hc_AF_.cif
Summary of feedback from opening /Users/sahtelis/Desktop/cx45_hc_AF_.cif
---
warnings | Unknown polymer entity '2' on line 26
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 1421
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '3' on line 2816
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '4' on line 4211
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '5' on line 5606
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '6' on line 7001
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for cx45_hc_AF_.cif
---
Chain | Description
2.2/A 2.1/B 2.3/C 2.4/D 2.5/E 2.6/F | No description available
Computing secondary structure
[Repeated 5 time(s)]
> hide #!2.1 models
> hide #!2 models
> hide #!1 models
> show #!2.1 models
> hide #!2.1 models
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> select subtract #2
Nothing selected
> hide #!4 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> color #2.2 #ec1478ff
> color #2.2 #eca6a6ff
> color #2.2 #ec9397ff
> color #2.3 #a0eca3ff
> color #2.4 #4472ecff
> color #2.5 #c9ec8aff
> color #2.6 #ec6635ff
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> view matrix models
> #2,0.87119,-0.18123,-0.45628,-5.2122,0.14082,0.98256,-0.12139,-6.9031,0.47032,0.041496,0.88152,-17.28
> view matrix models
> #2,0.15716,-0.43292,-0.88763,8.2651,0.12705,0.90019,-0.41655,-12.56,0.97937,-0.047311,0.19648,-47.312
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.15716,-0.43292,-0.88763,94.15,0.12705,0.90019,-0.41655,27.717,0.97937,-0.047311,0.19648,24.267
> show #!1 models
> view matrix models
> #2,0.15716,-0.43292,-0.88763,179.73,0.12705,0.90019,-0.41655,153.11,0.97937,-0.047311,0.19648,85.654
> view sel
> view matrix models
> #2,0.15716,-0.43292,-0.88763,167.47,0.12705,0.90019,-0.41655,183.56,0.97937,-0.047311,0.19648,117.43
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.47552,-0.87971,0.0014439,172.21,-0.86335,-0.46636,0.19269,222.44,-0.16883,-0.092873,-0.98126,131.9
> fitmap #2.1 inMap #1
Fit molecule cx45_hc_AF_.cif (#2.1) to map
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) using 1372 atoms
average map value = 0.9163, steps = 264
shifted from previous position = 29.6
rotated from previous position = 47.7 degrees
atoms outside contour = 1143, contour level = 1.62
Position of cx45_hc_AF_.cif (#2.1) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.60260083 0.69324780 -0.39532229 65.76738273
0.67836604 -0.18404942 0.71129833 -80.16709786
0.42034717 -0.69680218 -0.58118411 112.01489027
Axis -0.86526927 -0.50122396 -0.00914475
Axis point 0.00000000 -25.87389352 82.14196139
Rotation angle (degrees) 125.54318108
Shift along axis -17.74917362
> undo
> select subtract #2
Nothing selected
> close #2
> open /Users/sahtelis/Desktop/cx45_hc_AF_.cif
Summary of feedback from opening /Users/sahtelis/Desktop/cx45_hc_AF_.cif
---
warnings | Unknown polymer entity '2' on line 26
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 1421
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '3' on line 2816
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '4' on line 4211
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '5' on line 5606
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '6' on line 7001
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for cx45_hc_AF_.cif
---
Chain | Description
2.2/A 2.1/B 2.3/C 2.4/D 2.5/E 2.6/F | No description available
Computing secondary structure
[Repeated 5 time(s)]
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> close #4
> hide #!2 models
> hide #!2.1 models
> hide #!2.2 models
> close #2
> open /Users/sahtelis/Desktop/cx45_hc_AF_test2.cif
Summary of feedback from opening /Users/sahtelis/Desktop/cx45_hc_AF_test2.cif
---
warnings | Unknown polymer entity '2' on line 26
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 1421
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '3' on line 2816
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '4' on line 4211
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '5' on line 5606
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '6' on line 7001
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for cx45_hc_AF_test2.cif
---
Chain | Description
2.2/A 2.1/B 2.3/C 2.4/D 2.5/E 2.6/F | No description available
Computing secondary structure
[Repeated 5 time(s)]
> close #2
> open /Users/sahtelis/Desktop/cx45_hc_AF_test.cif
Summary of feedback from opening /Users/sahtelis/Desktop/cx45_hc_AF_test.cif
---
warnings | Unknown polymer entity '2' on line 26
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 1421
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '3' on line 2816
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '4' on line 4211
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '5' on line 5606
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '6' on line 7001
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for cx45_hc_AF_test.cif
---
Chain | Description
2.2/A 2.1/B 2.3/C 2.4/D 2.5/E 2.6/F | No description available
Computing secondary structure
[Repeated 5 time(s)]
> view
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,89.476,0,1,0,110.24,0,0,1,102.43
> view matrix models #2,1,0,0,153.61,0,1,0,179.1,0,0,1,177.93
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.67399,0.56926,-0.47083,156.75,-0.24391,0.77307,0.58555,197.38,0.69731,-0.27982,0.65989,148.4
> select subtract #2
Nothing selected
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> view matrix models
> #2,0.88646,0.33319,-0.3212,152,-0.19324,0.89712,0.39729,192.56,0.42052,-0.29011,0.85965,161.1
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.88646,0.33319,-0.3212,152.47,-0.19324,0.89712,0.39729,190.77,0.42052,-0.29011,0.85965,169.3
> ui mousemode right "rotate selected models"
> select subtract #2
Nothing selected
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> view matrix models
> #2,0.81682,0.31873,-0.48084,151.68,-0.057767,0.87451,0.48155,187.93,0.57399,-0.36556,0.73274,161.72
> select subtract #2
Nothing selected
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.81682,0.31873,-0.48084,143.9,-0.057767,0.87451,0.48155,190.29,0.57399,-0.36556,0.73274,158.27
> select subtract #2
Nothing selected
> color #2.2 #ec9a57ff
> color #2.3 #abec89ff
> color #2.4 #7ca6ecff
> color #2.4 #4069ecff
> color #2.5 #ecec4cff
> color #2.6 #ec33ceff
> color #2.6 #ec71ebff
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> select subtract #2
Nothing selected
> select add #2
8232 atoms, 8484 bonds, 6 pseudobonds, 1008 residues, 13 models selected
> select subtract #2
Nothing selected
> close #2
> open /Users/sahtelis/Desktop/cx45hexamer.pdb
Summary of feedback from opening /Users/sahtelis/Desktop/cx45hexamer.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
6855 messages similar to the above omitted
Chain information for cx45hexamer.pdb #2
---
Chain | Description
A B C D E F | No description available
> hide atoms
> show cartoons
Computing secondary structure
> select add #2
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models #2,1,0,0,112.54,0,1,0,225.03,0,0,1,45.373
> view matrix models #2,1,0,0,146.61,0,1,0,269.28,0,0,1,137.79
> view matrix models #2,1,0,0,165.73,0,1,0,215.65,0,0,1,202.25
> view matrix models #2,1,0,0,147.16,0,1,0,181.43,0,0,1,197.96
> view matrix models #2,1,0,0,145.1,0,1,0,175.22,0,0,1,187.16
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.9873,0.15867,-0.0077028,145.76,-0.11591,0.68637,-0.71795,164.34,-0.10863,0.70973,0.69605,186.61
> view matrix models
> #2,0.92398,0.22986,-0.30565,142.25,-0.38009,0.46354,-0.80041,170.49,-0.042299,0.85574,0.51567,181.47
> fitmap #2 inMap #1
Fit molecule cx45hexamer.pdb (#2) to map
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) using 8232 atoms
average map value = 1.088, steps = 156
shifted from previous position = 6.27
rotated from previous position = 40.3 degrees
atoms outside contour = 5978, contour level = 1.62
Position of cx45hexamer.pdb (#2) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.44191371 0.53530188 -0.71983621 178.36893378
0.39843855 0.83607177 0.37713486 175.89700398
0.80371573 -0.12014943 -0.58275649 129.29076421
Axis -0.30916257 -0.94719507 -0.08508818
Axis point 31.32362696 0.00000000 85.08028032
Rotation angle (degrees) 126.46269081
Shift along axis -232.75488966
> view matrix models
> #2,0.90004,-0.17218,-0.40036,143.42,0.17598,0.98401,-0.027578,173.48,0.39871,-0.045633,0.91594,168.83
> select subtract #2
Nothing selected
> fitmap #2 inMap #1
Fit molecule cx45hexamer.pdb (#2) to map
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) using 8232 atoms
average map value = 1.088, steps = 148
shifted from previous position = 1.63
rotated from previous position = 31.8 degrees
atoms outside contour = 5982, contour level = 1.62
Position of cx45hexamer.pdb (#2) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.12444344 0.99168025 -0.03292576 176.83945834
0.58190601 -0.04606353 0.81195045 174.78683595
0.80367855 -0.12020160 -0.58279701 129.28613561
Axis -0.70732778 -0.63482504 -0.31094144
Axis point -0.00000000 19.57136350 25.92767744
Rotation angle (degrees) 138.78205362
Shift along axis -276.24293874
> view
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> color #1 #c5912e80 models
> color #1 #c5b85e80 models
> color #1 #c5a87d80 models
> color #1 #fcd6a080 models
> color #1 #ebc89680 models
> color #1 #fbd6a080 models
> color #1 #f4cf9b80 models
> color #1 #efcb9880 models
> fitmap #2 inMap #1
Fit molecule cx45hexamer.pdb (#2) to map
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) using 8232 atoms
average map value = 1.088, steps = 40
shifted from previous position = 0.0397
rotated from previous position = 0.0268 degrees
atoms outside contour = 5984, contour level = 1.62
Position of cx45hexamer.pdb (#2) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.12421622 0.99169883 -0.03322258 176.85082416
0.58172741 -0.04565891 0.81210127 174.76158262
0.80384298 -0.12020264 -0.58256998 129.30024069
Axis -0.70719532 -0.63495266 -0.31098215
Axis point 0.00000000 19.53106454 25.93614613
Rotation angle (degrees) 138.76447276
Shift along axis -276.24347383
> color #1 #eea27380 models
> color #1 #eea61880 models
> color #1 #eec06780 models
> color #1 #eebf7680 models
> color #1 #eecd9280 models
> color #1 #eed9a080 models
> color #1 #eece9180 models
> color #1 #eebe8880 models
> color #1 #eeb47c80 models
> color #1 #eea66980 models
> color #1 #eeb97d80 models
> color #1 #eec48780 models
> color #1 #ffd29180 models
> color #1 #f5ca8b80 models
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> volume #1 level 1.65
> volume #1 level 1.6
> volume #1 level 1.63
> volume #1 level 1.7
> volume #1 level 1.8
> volume #1 level 1.9
> volume #1 level 1.7
> fitmap #2 inMap #1
Fit molecule cx45hexamer.pdb (#2) to map
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) using 8232 atoms
average map value = 1.088, steps = 48
shifted from previous position = 0.0463
rotated from previous position = 0.0333 degrees
atoms outside contour = 6192, contour level = 1.7
Position of cx45hexamer.pdb (#2) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.12403993 0.99171410 -0.03342495 176.83672499
0.58217497 -0.04545547 0.81179191 174.78633851
0.80354613 -0.12015378 -0.58298942 129.29785733
Axis -0.70716375 -0.63509668 -0.31075977
Axis point 0.00000000 19.53956707 25.96734789
Rotation angle (degrees) 138.78152605
Shift along axis -276.23931777
> select add #2
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.95191,0.059075,-0.30063,145.07,0.10453,0.85973,0.49993,185.93,0.28799,-0.50731,0.81222,166.7
> view matrix models
> #2,0.95191,0.059075,-0.30063,143.96,0.10453,0.85973,0.49993,186.69,0.28799,-0.50731,0.81222,166.93
> fitmap #2 inMap #1
Fit molecule cx45hexamer.pdb (#2) to map
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) using 8232 atoms
average map value = 1.088, steps = 40
shifted from previous position = 0.323
rotated from previous position = 0.0377 degrees
atoms outside contour = 6194, contour level = 1.7
Position of cx45hexamer.pdb (#2) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.12438142 0.99168994 -0.03286800 176.83475993
0.58202830 -0.04609228 0.81186116 174.78307940
0.80359959 -0.12011055 -0.58292464 129.28594977
Axis -0.70732477 -0.63484142 -0.31091483
Axis point 0.00000000 19.56882865 25.93278083
Rotation angle (degrees) 138.79154992
Shift along axis -276.23606454
> select subtract #2
Nothing selected
> save /Users/sahtelis/Desktop/cx45_map_model_20250324.cxs
> save /Users/sahtelis/Desktop/cx45modelintomap_20150324.png width 851 height
> 646 supersample 3
> select /D
1372 atoms, 1414 bonds, 1 pseudobond, 168 residues, 2 models selected
> color (#!2 & sel) cyan
> select add #2
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> select subtract #2
Nothing selected
> select /D
1372 atoms, 1414 bonds, 1 pseudobond, 168 residues, 2 models selected
> color (#!2 & sel) lime
> select add #2
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> select subtract #2
Nothing selected
> lighting simple
> select add #2
8232 atoms, 8487 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> view matrix models
> #2,0.95198,0.058915,-0.30044,144.61,0.10474,0.85943,0.50041,186.36,0.28769,-0.50785,0.81199,166.8
> view matrix models
> #2,0.95198,0.058915,-0.30044,141.01,0.10474,0.85943,0.50041,188.99,0.28769,-0.50785,0.81199,168.28
> fitmap #2 inMap #1
Fit molecule cx45hexamer.pdb (#2) to map
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) using 8232 atoms
average map value = 1.088, steps = 68
shifted from previous position = 4.25
rotated from previous position = 0.00599 degrees
atoms outside contour = 6191, contour level = 1.7
Position of cx45hexamer.pdb (#2) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.12447949 0.99167702 -0.03288675 176.84542423
0.58204575 -0.04613778 0.81184607 174.76118689
0.80357177 -0.12019978 -0.58294461 129.29296381
Axis -0.70736105 -0.63481660 -0.31088299
Axis point 0.00000000 19.56482633 25.94286233
Rotation angle (degrees) 138.79013195
Shift along axis -276.22985007
> view matrix models
> #2,0.95198,0.058815,-0.30047,142.69,0.10484,0.85943,0.5004,187.52,0.28766,-0.50787,0.81199,167.8
> select subtract #2
Nothing selected
> fitmap #2 inMap #1
Fit molecule cx45hexamer.pdb (#2) to map
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) using 8232 atoms
average map value = 1.088, steps = 56
shifted from previous position = 2
rotated from previous position = 0.0184 degrees
atoms outside contour = 6196, contour level = 1.7
Position of cx45hexamer.pdb (#2) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.12440432 0.99168312 -0.03298687 176.84516449
0.58182432 -0.04597806 0.81201384 174.76129764
0.80374375 -0.12021059 -0.58270523 129.28786916
Axis -0.70729807 -0.63484493 -0.31096841
Axis point 0.00000000 19.55183462 25.92889173
Rotation angle (degrees) 138.77604835
Shift along axis -276.23301056
> save /Users/sahtelis/Desktop/cx45_map_model_20250324.cxs
> save /Users/sahtelis/Desktop/cx45modelintomap_20150324.png width 851 height
> 646 supersample 3
> save /Users/sahtelis/Desktop/cx45_map_model_20250324_2.cxs includeMaps true
> ui tool show Axes/Planes/Centroids
> hide #!2 models
> hide #!1 models
> show #!2 models
> open /Users/sahtelis/Desktop/cx43_hc.pdb
Chain information for cx43_hc.pdb #3
---
Chain | Description
A B C D E F | No description available
> hide #!3 models
> hide #!2 models
> show #!1 models
> volume #1 level 1.039
> hide #!1 models
> open /Users/sahtelis/Downloads/cryosparc_P7_J67_004_volume_map.mrc
Opened cryosparc_P7_J67_004_volume_map.mrc as #4, grid size 192,192,192, pixel
1.84, shown at level 0.334, step 1, values float32
> volume #4 level 1.3
> surface dust #4 size 18.4
> volume #4 level 1.162
> volume #4 level 1.62
> volume #4 level 1.3
> volume #4 level 1.2
> volume #4 level 1.25
> volume #4 level 1.28
> volume #4 level 1.29
> volume #1 level 1.29
> show #!1 models
> hide #!4 models
> volume #1 level 1.676
> volume #1 level 1.311
> show #!4 models
> hide #!1 models
> volume #4 level 0.9911
> volume #4 level 0.7882
> show #!1 models
> hide #!4 models
> volume #1 level 0.9471
> show #!4 models
> fitmap #4 inMap #1
Fit map cryosparc_P7_J67_004_volume_map.mrc in map
cryosparc_P7_J67_004_volume_map_sharp.mrc using 31754 points
correlation = 0.4565, correlation about mean = 0.06607, overlap = 1.601e+04
steps = 88, shift = 2.89, angle = 10.8 degrees
Position of cryosparc_P7_J67_004_volume_map.mrc (#4) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.06446271 0.92365470 -0.37776519 64.87919714
0.26513899 0.34909405 0.89879623 -79.55125069
0.96205294 -0.15809912 -0.22239333 55.98553500
Axis -0.57780737 -0.73248198 -0.36001221
Axis point 38.82877710 0.00000000 76.54368923
Rotation angle (degrees) 113.85467924
Shift along axis 0.62670284
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.14886,0.39952,-0.90456,226.7,0.47092,0.77572,0.42011,-111.46,0.86953,-0.48851,-0.072662,107.17
> view matrix models
> #4,-0.70163,0.71239,-0.014849,175.46,0.70687,0.69327,-0.14039,-46.465,-0.089718,-0.109,-0.98998,360.32
> view matrix models
> #4,-0.02086,0.44736,0.89411,-47.352,0.45762,0.7994,-0.3893,19.722,-0.8889,0.40104,-0.2214,285.09
> fitmap #4 inMap #1
Fit map cryosparc_P7_J67_004_volume_map.mrc in map
cryosparc_P7_J67_004_volume_map_sharp.mrc using 31754 points
correlation = 0.7478, correlation about mean = 0.0328, overlap = 3.042e+04
steps = 72, shift = 3.52, angle = 5.96 degrees
Position of cryosparc_P7_J67_004_volume_map.mrc (#4) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84556251 0.53387641 -0.00000353 -67.02352335
-0.53387641 0.84556252 -0.00000184 121.58332153
0.00000200 0.00000344 0.99999999 0.56740782
Axis 0.00000494 -0.00000518 -1.00000000
Axis point 176.63951272 176.63878639 0.00000000
Rotation angle (degrees) 32.26774459
Shift along axis -0.56836914
> select subtract #4
Nothing selected
> volume #1 level 1.62
> volume #4 color #bfa1b8
> volume #4 color #bf81ad
> volume #4 color white
> volume #4 color #ffffffc0
> volume #4 color #ffffffbf
> hide #!1 models
> show #!1 models
> transparency #1,4 50
> transparency #1 50
> transparency #1 30
> transparency #4 90
> transparency #4 95
> transparency #1 0
> transparency #1 25
> transparency #1 10
> transparency #1 25
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> transparency #4 90
> color #4 silver models
> color #4 #d6d6d6ff models
> color #4 #ebebebff models
> color #4 white models
> color #4 #ebebebff models
> color #4 #d6d6d6ff models
> transparency #4 90
> transparency #1 30
> hide #!4 models
> hide #!1 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> show #!2 models
> save /Users/sahtelis/Desktop/image1.png supersample 3
> save /Users/sahtelis/Desktop/image2.png supersample 3
> hide #!4 models
> volume #1 level 1.234
> hide #!2 models
> close #4
> ui tool show "Segment Map"
[Repeated 1 time(s)]Segmenting cryosparc_P7_J67_004_volume_map_sharp.mrc,
density threshold 1.234194
Showing 24 region surfaces
405 watershed regions, grouped to 24 regions
Showing cryosparc_P7_J67_004_volume_map_sharp.seg - 24 regions, 24 surfaces
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #4.2 models
> hide #4.3 models
> show #4.3 models
> hide #4.4 models
> show #4.4 models
> hide #4.5 models
> hide #4.6 models
> hide #4.7 models
> hide #4.8 models
> hide #4.9 models
> show #4.9 models
> hide #4.10 models
> show #4.10 models
> hide #4.11 models
> show #4.11 models
> hide #4.12 models
> show #4.12 models
> hide #4.13 models
> hide #4.14 models
> hide #4.15 models
> hide #4.16 models
> hide #4.17 models
> hide #4.18 models
> show #4.1 models
> show #4.2 models
> hide #4.3 models
> hide #4.4 models
> show #4.3 models
> show #4.4 models
> show #4.5 models
> show #4.6 models
> show #4.7 models
> show #4.8 models
> hide #4.9 models
> hide #4.10 models
> hide #4.11 models
> hide #4.12 models
> show #4.13 models
> show #4.14 models
> show #4.15 models
> show #4.16 models
> show #4.17 models
> show #4.18 models
> hide #4.19 models
> hide #4.20 models
> hide #4.21 models
> hide #4.22 models
> hide #4.23 models
> hide #4.24 models
> hide #4.14 models
> show #4.14 models
> hide #4.6 models
> show #4.6 models
> hide #4.3 models
> hide #4.2 models
> show #4.2 models
> hide #4.4 models
> hide #4.1 models
> hide #4.2 models
> show #4.3 models
> show #4.4 models
> hide #4.5 models
> hide #4.6 models
> hide #4.7 models
> hide #4.8 models
> show #4.9 models
> show #4.10 models
> show #4.11 models
> show #4.12 models
> hide #4.13 models
> hide #4.14 models
> hide #4.15 models
> hide #4.16 models
> hide #4.17 models
> hide #4.18 models
> show #4.19 models
> show #4.20 models
> show #4.21 models
> show #4.22 models
> show #4.23 models
> show #4.24 models
> volume gaussian #4 sDev 2.
> volume gaussian #4 sDev 2
> hide #!4 models
> show #!4 models
> volume gaussian #4 sDev 5
[Repeated 1 time(s)]
> hide #!4 models
> show #!1 models
> volume gaussian #1 sDev 5
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc gaussian as #5, grid size
192,192,192, pixel 1.84, shown at step 1, values float32
> volume gaussian #1 sDev 0
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/gaussian.py:118: RuntimeWarning: invalid value
encountered in scalar divide
u = min(i,size-i) / sdev
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/gaussian.py:118: RuntimeWarning: divide by zero
encountered in scalar divide
u = min(i,size-i) / sdev
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc gaussian as #6, grid size
192,192,192, pixel 1.84, shown at step 1, values float32
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/arrays.py:172: RuntimeWarning: invalid value
encountered in multiply
v = fbc + b * bsize # Center of bin where rank crossed.
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/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2773, in update_histogram
counts = s.bin_counts(bins)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/arrays.py", line 138, in bin_counts
b0 = int(ceil(fb0))
^^^^^^^^^
ValueError: cannot convert float NaN to integer
ValueError: cannot convert float NaN to integer
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/arrays.py", line 138, in bin_counts
b0 = int(ceil(fb0))
^^^^^^^^^
See log for complete Python traceback.
> volume gaussian #1 sDev 1
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc gaussian as #7, grid size
192,192,192, pixel 1.84, shown at step 1, values float32
> show #!1 models
> close #7
> close #6
> close #5
> ui tool show Segmentations
> ui view fourup
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/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
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/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
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/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple
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: MacBook Air
Model Identifier: Mac15,12
Model Number: MC8G4KS/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 5 days, 19 hours, 50 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → volume gaussian: update histogram: cannot convert float NaN to integer |
comment:2 by , 7 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
User tried to use volume gaussian with smoothing standard deviation 0 which does not make sense. I made the volume gaussian code give an error if standard deviation <= 0.