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Opened 7 months ago
Closed 7 months ago
#17259 closed defect (duplicate)
'ArrayGridData' object has no attribute 'dicom_data'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.11.0-21-generic-x86_64-with-glibc2.39
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 /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/Pavol/NL-
> refine_3.31A_nucleosome_session.cxs
Opened cryosparc_P12_J159_006_volume_map.mrc x flip as #11, grid size
256,256,256, pixel 0.85, shown at level 0.0646, step 1, values float32
Opened cryosparc_P12_J276_006_volume_map.mrc x flip as #13, grid size
256,256,256, pixel 0.85, shown at level 0.0618, step 1, values float32
Log from Tue Apr 1 09:44:49 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/Pavol/ab-
> initio_nucleosome_session.cxs
Opened cryosparc_P12_J135_008_volume_map.mrc as #1, grid size 256,256,256,
pixel 0.85, shown at level 0.0602, step 1, values float32
Opened cryosparc_P12_J156_008_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.0484, step 1, values float32
Opened cryosparc_P12_J157_006_volume_map.mrc as #3, grid size 256,256,256,
pixel 0.85, shown at level 0.051, step 1, values float32
Opened cryosparc_P12_J158_006_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.85, shown at level 0.0527, step 1, values float32
Opened cryosparc_P12_J159_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.85, shown at level 0.0798, step 1, values float32
Opened cryosparc_P12_J160_008_volume_map.mrc as #6, grid size 256,256,256,
pixel 0.85, shown at level 0.05, step 1, values float32
Opened cryosparc_P12_J161_007_volume_map.mrc as #7, grid size 256,256,256,
pixel 0.85, shown at level 0.0475, step 1, values float32
Opened cryosparc_P12_J162_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.85, shown at level 0.0495, step 1, values float32
Opened cryosparc_P12_J163_007_volume_map.mrc as #9, grid size 256,256,256,
pixel 0.85, shown at level 0.047, step 1, values float32
Opened cryosparc_P12_J159_006_volume_map.mrc x flip as #11, grid size
256,256,256, pixel 0.85, shown at level 0.0646, step 1, values float32
Log from Sun Mar 30 23:04:18 2025 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
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J135_008_volume_map.mrc
Opened cryosparc_P12_J135_008_volume_map.mrc as #1, grid size 256,256,256,
pixel 0.85, shown at level 0.0602, step 1, values float32
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J156_008_volume_map.mrc
Opened cryosparc_P12_J156_008_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.0484, step 1, values float32
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J157_006_volume_map.mrc
Opened cryosparc_P12_J157_006_volume_map.mrc as #3, grid size 256,256,256,
pixel 0.85, shown at level 0.051, step 1, values float32
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J158_006_volume_map.mrc
Opened cryosparc_P12_J158_006_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.85, shown at level 0.0527, step 1, values float32
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J159_006_volume_map.mrc
Opened cryosparc_P12_J159_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.85, shown at level 0.0798, step 1, values float32
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J160_008_volume_map.mrc
Opened cryosparc_P12_J160_008_volume_map.mrc as #6, grid size 256,256,256,
pixel 0.85, shown at level 0.05, step 1, values float32
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J161_007_volume_map.mrc
Opened cryosparc_P12_J161_007_volume_map.mrc as #7, grid size 256,256,256,
pixel 0.85, shown at level 0.0475, step 1, values float32
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J162_007_volume_map.mrc
Opened cryosparc_P12_J162_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.85, shown at level 0.0495, step 1, values float32
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/J159/cryosparc_P12_J163_007_volume_map.mrc
Opened cryosparc_P12_J163_007_volume_map.mrc as #9, grid size 256,256,256,
pixel 0.85, shown at level 0.047, step 1, values float32
> hide #!1 models
> show #!1 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!6 models
> hide #!9 models
> hide #!6 models
> show #!5 models
> open 3afa fromDatabase pdb format mmcif
3afa title:
The human nucleosome structure [more info...]
Chain information for 3afa #10
---
Chain | Description | UniProt
A E | Histone H3.1 | H31_HUMAN 0-135
B F | Histone H4 | H4_HUMAN 0-102
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125
I J | 146-MER DNA |
Non-standard residues in 3afa #10
---
CL — chloride ion
MN — manganese (II) ion
> select #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.98568,0.030299,-0.16589,17.265,0.16857,-0.1496,0.97427,-7.6787,0.0047023,-0.98828,-0.15257,235.58
> view matrix models
> #5,0.039545,-0.37377,0.92668,38.648,-0.99682,0.049472,0.062492,202.23,-0.069203,-0.9262,-0.37062,261.92
> ui mousemode right "move picked models"
> view matrix models
> #5,0.039545,-0.37377,0.92668,-92.687,-0.99682,0.049472,0.062492,146.76,-0.069203,-0.9262,-0.37062,265.94
> view matrix models
> #5,0.039545,-0.37377,0.92668,-84.75,-0.99682,0.049472,0.062492,167.34,-0.069203,-0.9262,-0.37062,202.71
> view matrix models
> #5,0.039545,-0.37377,0.92668,-92.871,-0.99682,0.049472,0.062492,165.73,-0.069203,-0.9262,-0.37062,207.61
> vop zflip #5
> volume zflip #5
Expected a density maps specifier or a keyword
> ui tool show "Show Volume Menu"
> vop zflip #5
> volume zflip #5
Expected a density maps specifier or a keyword
> vop #5 zflip
> volume #5 zflip
Expected a keyword
> volume #5 zflip
Expected a keyword
> volume #5 flipNormals z
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> volume #5 flipNormals axis x
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> volume resample #5 originIndex yx- z
Expected a keyword
> volume flip #5 axis x
Opened cryosparc_P12_J159_006_volume_map.mrc x flip as #11, grid size
256,256,256, pixel 0.85, shown at step 1, values float32
> ui mousemode right "rotate selected models"
> select #11
2 models selected
> view matrix models
> #11,0.039126,-0.088513,0.99531,-130.87,-0.99471,0.091242,0.047217,162.82,-0.094993,-0.99189,-0.084475,184.73
> view matrix models
> #11,0.034013,0.19147,0.98091,-158.33,-0.99644,0.082309,0.018485,167.23,-0.077198,-0.97804,0.19358,149.64
> ui mousemode right "move picked models"
> view matrix models
> #11,0.034013,0.19147,0.98091,-157.64,-0.99644,0.082309,0.018485,76.402,-0.077198,-0.97804,0.19358,140.74
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.035755,0.18213,0.98263,-157.03,-0.99572,0.090302,0.019494,75.364,-0.085183,-0.97912,0.18458,142.75
> view matrix models
> #11,0.041006,0.21006,0.97683,-159.9,-0.98818,0.15305,0.0085707,69.15,-0.1477,-0.96563,0.21385,144.71
> view matrix models
> #11,0.11681,0.20555,0.97165,-166.99,-0.98387,0.1574,0.084982,59.513,-0.13547,-0.96591,0.22062,142.65
> ui mousemode right "move picked models"
> select #11
2 models selected
> select clear
> select #11
2 models selected
> select add #10
12198 atoms, 12811 bonds, 362 pseudobonds, 1245 residues, 5 models selected
> select subtract #10
2 models selected
> select subtract #11
Nothing selected
> select add #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.12891,0.2048,0.97028,-168.06,-0.98263,0.15807,0.097184,57.918,-0.13347,-0.96596,0.22162,142.33
> ui mousemode right "move picked models"
> select subtract #11
Nothing selected
> select add #11
2 models selected
> select subtract #11
Nothing selected
> select add #11
2 models selected
> view matrix models
> #11,0.12891,0.2048,0.97028,-165.42,-0.98263,0.15807,0.097184,58.151,-0.13347,-0.96596,0.22162,134.24
> view matrix models
> #11,0.12891,0.2048,0.97028,-162.52,-0.98263,0.15807,0.097184,58.636,-0.13347,-0.96596,0.22162,136.52
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.096255,0.22192,0.9703,-160.82,-0.99383,0.075465,0.081329,70.399,-0.055176,-0.97214,0.22781,128.04
> view matrix models
> #11,0.0767,0.14969,0.98575,-152.82,-0.99547,0.067286,0.067238,73.048,-0.056263,-0.98644,0.15417,138.06
> view matrix models
> #11,0.056699,0.13227,0.98959,-149.26,-0.99608,0.074967,0.04705,74.602,-0.067964,-0.98837,0.136,141.6
> view matrix models
> #11,-0.062798,0.13734,0.98853,-136.8,-0.98908,0.12376,-0.080027,83.167,-0.13334,-0.98276,0.12806,148.95
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> ui mousemode right "move picked models"
> view matrix models
> #11,-0.062798,0.13734,0.98853,-138.27,-0.98908,0.12376,-0.080027,80.373,-0.13334,-0.98276,0.12806,149.14
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.10841,0.12578,0.98612,-155.21,-0.98577,0.14179,0.090287,58.69,-0.12846,-0.98187,0.13936,147.23
> hide atoms
> show cartoons
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> ui tool show "Fit in Map"
> fitmap #10 inMap #1
Fit molecule 3afa (#10) to map cryosparc_P12_J135_008_volume_map.mrc (#1)
using 12198 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 12198, contour level = 0.060212
Position of 3afa (#10) relative to cryosparc_P12_J135_008_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> fitmap #10 inMap #1
Fit molecule 3afa (#10) to map cryosparc_P12_J135_008_volume_map.mrc (#1)
using 12198 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 12198, contour level = 0.060212
Position of 3afa (#10) relative to cryosparc_P12_J135_008_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> fitmap #10 inMap #11
Fit molecule 3afa (#10) to map cryosparc_P12_J159_006_volume_map.mrc x flip
(#11) using 12198 atoms
average map value = 0.08045, steps = 104
shifted from previous position = 3.96
rotated from previous position = 6.18 degrees
atoms outside contour = 6510, contour level = 0.079765
Position of 3afa (#10) relative to cryosparc_P12_J159_006_volume_map.mrc x
flip (#11) coordinates:
Matrix rotation and translation
0.09830838 -0.99406054 -0.04668101 91.77501364
0.20198674 0.06586352 -0.97717110 158.75044052
0.97444180 0.08663516 0.20726198 123.92342806
Axis 0.56029358 -0.53781274 0.62994329
Axis point -113.83818261 170.72270443 0.00000000
Rotation angle (degrees) 108.31753816
Shift along axis 44.10767358
> fitmap #10 inMap #11
Fit molecule 3afa (#10) to map cryosparc_P12_J159_006_volume_map.mrc x flip
(#11) using 12198 atoms
average map value = 0.08045, steps = 40
shifted from previous position = 0.00448
rotated from previous position = 0.00658 degrees
atoms outside contour = 6514, contour level = 0.079765
Position of 3afa (#10) relative to cryosparc_P12_J159_006_volume_map.mrc x
flip (#11) coordinates:
Matrix rotation and translation
0.09832350 -0.99405397 -0.04678877 91.78105923
0.20194088 0.06596853 -0.97717349 158.74802611
0.97444978 0.08663055 0.20722640 123.92292441
Axis 0.56028416 -0.53786577 0.62990640
Axis point -113.84530162 170.74040419 -0.00000000
Rotation angle (degrees) 108.31498696
Shift along axis 44.09818717
> volume #11 level 0.06907
> volume #11 style mesh
> volume #11 level 0.08422
Drag select of 14 residues, 11 cryosparc_P12_J159_006_volume_map.mrc x flip
> select clear
> volume #11 level 0.1314
> volume #11 level 0.09313
> volume #11 level 0.06373
> volume #11 level 0.06818
> volume #11 level 0.06462
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> hide #!11 models
> hide #!10 models
> show #!9 models
> show #!10 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!6 models
> show #!5 models
> select add #9
2 models selected
> select add #8
4 models selected
> select add #7
6 models selected
> select add #6
8 models selected
> select add #5
10 models selected
> select add #4
12 models selected
> select add #3
14 models selected
> select add #2
16 models selected
> select add #1
18 models selected
> show #!2 models
> show #!3 models
> show #!4 models
> show #!1 models
> hide #!10 models
> show #!10 models
> view matrix models
> #1,0.99294,-0.0090486,-0.11823,11.296,0.0049201,0.99937,-0.035164,2.8576,0.11848,0.034334,0.99236,-7.7783,#2,0.99294,-0.0090486,-0.11823,11.296,0.0049201,0.99937,-0.035164,2.8576,0.11848,0.034334,0.99236,-7.7783,#3,0.99294,-0.0090486,-0.11823,11.296,0.0049201,0.99937,-0.035164,2.8576,0.11848,0.034334,0.99236,-7.7783,#4,0.99294,-0.0090486,-0.11823,11.296,0.0049201,0.99937,-0.035164,2.8576,0.11848,0.034334,0.99236,-7.7783,#5,0.056467,-0.26207,0.96339,-106.97,-0.99356,0.080171,0.080045,160.72,-0.098214,-0.96171,-0.25586,192.94,#6,0.99294,-0.0090486,-0.11823,11.296,0.0049201,0.99937,-0.035164,2.8576,0.11848,0.034334,0.99236,-7.7783,#7,0.99294,-0.0090486,-0.11823,11.296,0.0049201,0.99937,-0.035164,2.8576,0.11848,0.034334,0.99236,-7.7783,#8,0.99294,-0.0090486,-0.11823,11.296,0.0049201,0.99937,-0.035164,2.8576,0.11848,0.034334,0.99236,-7.7783,#9,0.99294,-0.0090486,-0.11823,11.296,0.0049201,0.99937,-0.035164,2.8576,0.11848,0.034334,0.99236,-7.7783
> undo
[Repeated 1 time(s)]
> show #!11 models
> show #!10 models
> hide #!10 models
> hide #!11 models
> select subtract #1
16 models selected
> select subtract #2
14 models selected
> select subtract #3
12 models selected
> select subtract #4
10 models selected
> select subtract #5
8 models selected
> select subtract #6
6 models selected
> select subtract #7
4 models selected
> select subtract #8
2 models selected
> select subtract #9
Nothing selected
> hide #!2 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide all
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!11 models
> show #!10 models
> hide #!11 models
> hide #!10 models
> show #!5 models
> hide #!5 models
> show #!10 models
> show #!11 models
> hide #!10 models
> show #!10 models
> surface dust #11 size 8.5
> hide #!11 models
> show atoms
> style ball
Changed 12198 atom styles
> show #!11 models
> hide #!10 models
> volume #!11 style surface
> volume #!11 style mesh
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> save /home/paloha/Desktop/ab-initio_nucleosome_session.cxs
——— End of log from Sun Mar 30 23:04:18 2025 ———
opened ChimeraX session
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/Pavol/cryosparc_P12_J276_006_volume_map.mrc
File size 19169280 too small for grid size (256,256,256)
> open
> /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/Pavol/cryosparc_P12_J276_006_volume_map.mrc
Opened cryosparc_P12_J276_006_volume_map.mrc as #12, grid size 256,256,256,
pixel 0.85, shown at level 0.0809, step 1, values float32
> select add #12
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,-207.01,0,1,0,-159.26,0,0,1,41.054
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.48604,-0.60901,0.6268,-157.49,-0.53142,0.36343,0.76519,-120.66,-0.69381,-0.705,-0.147,322.37
> view matrix models
> #12,0.71119,-0.38221,0.59002,-201.99,-0.64345,-0.015853,0.76532,-67.978,-0.28316,-0.92394,-0.25721,313.72
> view matrix models
> #12,0.74145,-0.33648,0.58055,-209.08,-0.58046,0.11243,0.80649,-93.217,-0.33664,-0.93496,-0.11195,304.16
> view matrix models
> #12,0.75055,-0.2859,0.59577,-217.21,-0.58079,0.14465,0.8011,-96.01,-0.31521,-0.94728,-0.057479,296.95
> view matrix models
> #12,0.074215,0.05648,-0.99564,0.88248,0.98603,-0.15345,0.064794,-150.45,-0.14913,-0.98654,-0.06708,284.2
> view matrix models
> #12,0.082034,0.010376,-0.99658,5.0669,0.99334,0.080265,0.082604,-178.25,0.080847,-0.99672,-0.0037221,253.1
> view matrix models
> #12,-0.9215,-0.21057,0.32633,-12.998,-0.35159,0.095405,-0.93128,81.652,0.16497,-0.97291,-0.16195,259.44
> view matrix models
> #12,-0.97948,-0.19502,-0.050908,34.597,0.019331,0.16052,-0.98684,40.741,0.20062,-0.96757,-0.15346,254.03
> view matrix models
> #12,-0.98348,-0.17559,-0.043955,32.164,0.055697,-0.062506,-0.99649,61.724,0.17223,-0.98248,0.071254,233.12
> volume flip #12 axis x
Opened cryosparc_P12_J276_006_volume_map.mrc x flip as #13, grid size
256,256,256, pixel 0.85, shown at step 1, values float32
> select add #13
4 models selected
> select subtract #12
2 models selected
> view matrix models
> #13,-0.97826,-0.20241,-0.045088,34.595,0.041106,0.023837,-0.99887,54.346,0.20326,-0.97901,-0.014998,239.21
> view matrix models
> #13,0.058912,0.047989,0.99711,-223.03,-0.99565,-0.069438,0.062168,55.608,0.072221,-0.99643,0.04369,248.56
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.058912,0.047989,0.99711,-137.21,-0.99565,-0.069438,0.062168,71.11,0.072221,-0.99643,0.04369,246.89
> view matrix models
> #13,0.058912,0.047989,0.99711,-136.65,-0.99565,-0.069438,0.062168,71.117,0.072221,-0.99643,0.04369,246.87
> view matrix models
> #13,0.058912,0.047989,0.99711,-143.6,-0.99565,-0.069438,0.062168,72.018,0.072221,-0.99643,0.04369,136.87
> view matrix models
> #13,0.058912,0.047989,0.99711,-143.86,-0.99565,-0.069438,0.062168,87.194,0.072221,-0.99643,0.04369,138.26
> hide #!11 models
> hide #!10 models
> show #!10 models
> fitmap #10 inMap #13
Fit molecule 3afa (#10) to map cryosparc_P12_J276_006_volume_map.mrc x flip
(#13) using 12198 atoms
average map value = 0.0826, steps = 124
shifted from previous position = 1.85
rotated from previous position = 11.5 degrees
atoms outside contour = 6635, contour level = 0.080854
Position of 3afa (#10) relative to cryosparc_P12_J276_006_volume_map.mrc x
flip (#13) coordinates:
Matrix rotation and translation
0.08052403 -0.99675229 0.00086889 89.48743705
0.23613048 0.01822921 -0.97155035 157.17273862
0.96837920 0.07843833 0.23683149 123.31546929
Axis 0.55660607 -0.51288373 0.65355946
Axis point -106.73248114 160.43195029 0.00000000
Rotation angle (degrees) 109.40282480
Shift along axis 49.79190155
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.08288,-0.029909,0.99611,-138.01,-0.99495,-0.059192,0.081006,83.878,0.056539,-0.9978,-0.034664,149.03
> volume sel style mesh
> volume sel style image
> volume sel style surface
> transparency sel 50
> view matrix models
> #13,0.059191,-0.094195,0.99379,-128.31,-0.99255,-0.11177,0.048522,92.937,0.10651,-0.98926,-0.10011,150.16
> fitmap #10 inMap #13
Fit molecule 3afa (#10) to map cryosparc_P12_J276_006_volume_map.mrc x flip
(#13) using 12198 atoms
average map value = 0.0826, steps = 112
shifted from previous position = 0.382
rotated from previous position = 8.52 degrees
atoms outside contour = 6640, contour level = 0.080854
Position of 3afa (#10) relative to cryosparc_P12_J276_006_volume_map.mrc x
flip (#13) coordinates:
Matrix rotation and translation
0.08049822 -0.99675436 0.00087933 89.49706134
0.23613457 0.01821322 -0.97154966 157.17479396
0.96838035 0.07841565 0.23683429 123.31225755
Axis 0.55659774 -0.51288254 0.65356748
Axis point -106.72329831 160.43451060 0.00000000
Rotation angle (degrees) 109.40400958
Shift along axis 49.79453569
> view matrix models
> #13,0.07441,-0.098187,0.99238,-129.37,-0.99232,-0.10585,0.063933,90.525,0.098767,-0.98952,-0.10531,151.62
> view matrix models
> #13,0.035789,-0.065068,0.99724,-129.29,-0.99936,-0.0017165,0.035753,83.366,-0.0006146,-0.99788,-0.065087,158.68
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!13 models
> show #!10 models
> hide #!10 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!10 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!13 models
> hide #!10 models
> show #!13 models
> hide #!13 models
> show #!13 models
> fitmap #11 inMap #13
Fit map cryosparc_P12_J159_006_volume_map.mrc x flip in map
cryosparc_P12_J276_006_volume_map.mrc x flip using 227219 points
correlation = 0.9726, correlation about mean = 0.8239, overlap = 2957
steps = 116, shift = 2.02, angle = 14 degrees
Position of cryosparc_P12_J159_006_volume_map.mrc x flip (#11) relative to
cryosparc_P12_J276_006_volume_map.mrc x flip (#13) coordinates:
Matrix rotation and translation
0.99999386 -0.00218209 0.00273964 -0.10488207
0.00220027 0.99997546 -0.00665164 0.40325296
-0.00272506 0.00665763 0.99997412 0.29267643
Axis 0.88491867 0.36334234 0.29137827
Axis point 0.00000000 -37.67154607 53.17155909
Rotation angle (degrees) 0.43087107
Shift along axis 0.13898633
> volume #13 change image level -0.003445,0 level 0.08082,0.8 level 0.4017,1
> volume #13 level 0.06473
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> movie record
> turn y 2 180
> wait 180
> movie encode /home/paloha/Desktop/movie1.mp4
Movie saved to /home/paloha/Desktop/movie1.mp4
> hide cartoons
> show cartoons
> show atoms
> hide atoms
> show atoms
> style sphere
Changed 12198 atom styles
> style ball
Changed 12198 atom styles
> style stick
Changed 12198 atom styles
> style ball
Changed 12198 atom styles
> hide #!13 models
> cofr sel
> view #10 clip false
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> volume #13 level 0.08201
> surface dust #13 size 8.5
> hide #!10 models
> color #13 #f6d32dff models
> volume sel show
> volume sel hide
> volume sel show
> volume sel style surface
> lighting soft
> lighting full
> graphics silhouettes true
> lighting flat
> lighting full
> view orient
[Repeated 1 time(s)]
> show #!10 models
> fitmap #10 inMap #13
Fit molecule 3afa (#10) to map cryosparc_P12_J276_006_volume_map.mrc x flip
(#13) using 12198 atoms
average map value = 0.0826, steps = 100
shifted from previous position = 0.317
rotated from previous position = 6.6 degrees
atoms outside contour = 6723, contour level = 0.082006
Position of 3afa (#10) relative to cryosparc_P12_J276_006_volume_map.mrc x
flip (#13) coordinates:
Matrix rotation and translation
0.08031736 -0.99676898 0.00085271 89.48193936
0.23608678 0.01819219 -0.97156167 157.17239477
0.96840702 0.07823458 0.23678513 123.31584992
Axis 0.55653421 -0.51293484 0.65358054
Axis point -106.70475804 160.43198503 0.00000000
Rotation angle (degrees) 109.41163501
Shift along axis 49.77740298
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.013036,-0.21508,0.97651,-108.43,-0.9996,-0.027438,0.0073011,89.383,0.025223,-0.97621,-0.21535,170.69
> view matrix models
> #13,-0.016605,0.010243,0.99981,-131.96,-0.99951,0.026536,-0.016872,86.358,-0.026704,-0.9996,0.0097975,153.16
> view orient
[Repeated 1 time(s)]
> movie record
> turn y 2 180
> wait 180
> movie encode /home/paloha/Desktop/movie2.mp4
Movie saved to /home/paloha/Desktop/movie2.mp4
> select add #13
3 models selected
> select clear
> select add #13
3 models selected
> select add #13
3 models selected
> select add #10
12198 atoms, 12811 bonds, 362 pseudobonds, 1245 residues, 6 models selected
> select subtract #10
3 models selected
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> select add #10
12198 atoms, 12811 bonds, 362 pseudobonds, 1245 residues, 6 models selected
> select clear
> select add #10
12198 atoms, 12811 bonds, 362 pseudobonds, 1245 residues, 3 models selected
> mlp sel
Map values for surface "3afa_A SES surface": minimum -27.87, mean -2.292,
maximum 22.6
Map values for surface "3afa_B SES surface": minimum -27.6, mean -2.265,
maximum 22.71
Map values for surface "3afa_C SES surface": minimum -26.28, mean -3.202,
maximum 22.09
Map values for surface "3afa_D SES surface": minimum -27.28, mean -2.998,
maximum 22.13
Map values for surface "3afa_E SES surface": minimum -27.42, mean -2.376,
maximum 22.86
Map values for surface "3afa_F SES surface": minimum -28.85, mean -2.312,
maximum 22.88
Map values for surface "3afa_G SES surface": minimum -26.28, mean -3.176,
maximum 22.53
Map values for surface "3afa_H SES surface": minimum -24.5, mean -2.777,
maximum 21.67
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 3afa_A SES surface #10.3: minimum, -15.79, mean 1.62,
maximum 12.09
Coulombic values for 3afa_B SES surface #10.4: minimum, -8.60, mean 2.94,
maximum 17.85
Coulombic values for 3afa_C SES surface #10.5: minimum, -16.92, mean 2.37,
maximum 16.28
Coulombic values for 3afa_D SES surface #10.6: minimum, -8.88, mean 1.87,
maximum 10.28
Coulombic values for 3afa_E SES surface #10.7: minimum, -15.84, mean 1.62,
maximum 12.19
Coulombic values for 3afa_F SES surface #10.8: minimum, -9.37, mean 3.40,
maximum 14.50
Coulombic values for 3afa_G SES surface #10.9: minimum, -17.49, mean 1.95,
maximum 17.32
Coulombic values for 3afa_H SES surface #10.10: minimum, -9.14, mean 1.39,
maximum 14.29
Coulombic values for 3afa_I SES surface #10.11: minimum, -33.04, mean -15.07,
maximum -3.79
Coulombic values for 3afa_J SES surface #10.12: minimum, -29.22, mean -15.08,
maximum -3.93
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
[Repeated 1 time(s)]
> color sel bychain
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> hide #!13 models
> show #!13 models
> hide #!13 models
> nucleotides sel atoms
> style nucleic & sel stick
Changed 5980 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 5980 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 5980 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape muffler
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel ladder
> nucleotides sel fill
> style nucleic & sel stick
Changed 5980 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 5980 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape ellipsoid
> show #!13 models
> hide #!13 models
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> hbonds sel reveal true
1689 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
1689 hydrogen bonds found
> ~hbonds
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ~hbonds
> style sel ball
Changed 12198 atom styles
> style sel stick
Changed 12198 atom styles
> graphics silhouettes false
> graphics silhouettes true
> select subtract #10
10 models selected
> show #!13 models
> transparency #10.3-12#13.1 50
> show #!7 models
> hide #!7 models
> select add #1
2 models selected
> select add #2
4 models selected
> select add #3
6 models selected
> select add #4
8 models selected
> select add #5
10 models selected
> select add #7
12 models selected
> select add #6
14 models selected
> select add #8
16 models selected
> select add #9
18 models selected
> close #6
> close #1
> close #2
> close #4
> close #3
> close #5
> close #7
> close #8
> close #9
> close #12
> show #!11 models
> hide #!11 models
> volume #!13 style mesh
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> select add #13
3 models selected
> view matrix models
> #13,-0.016605,0.010243,0.99981,-131.35,-0.99951,0.026536,-0.016872,88.51,-0.026704,-0.9996,0.0097975,152.97
> volume sel style surface
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.15768,0.068273,0.98513,-154.73,-0.968,-0.18656,0.16786,86.828,0.19524,-0.98007,0.036672,123.82
> view matrix models
> #13,0.16704,0.051175,0.98462,-153.86,-0.96704,-0.18617,0.17373,86.014,0.19219,-0.98118,0.018392,126.35
> view matrix models
> #13,0.034907,-0.067915,0.99708,-128.26,-0.98922,0.13961,0.044141,68.361,-0.1422,-0.98787,-0.06231,172.42
> view matrix models
> #13,0.0073764,-0.04783,0.99883,-127.63,-0.99923,0.03805,0.0092015,84.279,-0.038446,-0.99813,-0.047513,160.61
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #13,0.0073764,-0.04783,0.99883,-127.54,-0.99923,0.03805,0.0092015,82.668,-0.038446,-0.99813,-0.047513,160.56
> fitmap #10 inMap #13
Fit molecule 3afa (#10) to map cryosparc_P12_J276_006_volume_map.mrc x flip
(#13) using 12198 atoms
average map value = 0.0826, steps = 76
shifted from previous position = 1.01
rotated from previous position = 2.91 degrees
atoms outside contour = 6720, contour level = 0.082006
Position of 3afa (#10) relative to cryosparc_P12_J276_006_volume_map.mrc x
flip (#13) coordinates:
Matrix rotation and translation
0.08049076 -0.99675497 0.00086955 89.49058821
0.23610990 0.01821897 -0.97155555 157.17482280
0.96838698 0.07840655 0.23681018 123.31924543
Axis 0.55659872 -0.51289371 0.65355788
Axis point -106.73018004 160.43607847 0.00000000
Rotation angle (degrees) 109.40479371
Shift along axis 49.79263318
> volume #13 level 0.04048
> volume #13 level 0.1426
> volume #13 level 0.1213
> volume #13 level 0.02813
> hide #!10 models
> volume #13 level 0.03487
> show #!10 models
> volume #13 level 0.04048
> view orient
> movie record
> turn y 2 180
> wait 180
> movie encode /home/paloha/Desktop/movie3.mp4
Movie saved to /home/paloha/Desktop/movie3.mp4
> hide #!10 models
> show #!11 models
> fitmap #11 inMap #13
Fit map cryosparc_P12_J159_006_volume_map.mrc x flip in map
cryosparc_P12_J276_006_volume_map.mrc x flip using 227219 points
correlation = 0.9726, correlation about mean = 0.8238, overlap = 2958
steps = 60, shift = 0.985, angle = 2.91 degrees
Position of cryosparc_P12_J159_006_volume_map.mrc x flip (#11) relative to
cryosparc_P12_J276_006_volume_map.mrc x flip (#13) coordinates:
Matrix rotation and translation
0.99999315 -0.00214229 0.00301766 -0.12206388
0.00216261 0.99997489 -0.00674846 0.41781492
-0.00300312 0.00675494 0.99997267 0.31971493
Axis 0.87691126 0.39098932 0.27956035
Axis point 0.00000000 -41.08358452 53.62386932
Rotation angle (degrees) 0.44114835
Shift along axis 0.14570159
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> volume #13 level 0.0618
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!13 models
> show #!13 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume sel style mesh
> show #!10 models
> color #13 #e01b24ff models
> color #13 #986a44ff models
> color #13 #1c71d8ff models
> color #13 #1a5fb4ff models
> color #13 #f9f06bff models
> color #13 white models
> color #13 #77767bff models
> color #13 white models
> color #13 #77767bff models
> color #13 black models
> color #13 #241f31ff models
> color #13 #5e5c64ff models
> color #13 #77767bff models
> color #13 white models
> color #13 #f6f5f4ff models
> color #13 #b2b2b280 models
> color #13 #f6d32d80 models
> color #13 #b2ffffff models
> color #13 #f9f06bff models
> color #13 #b2ffffff models
> color #13 white models
> transparency sel 50
> view orient
> movie record
> turn y 2 180
> wait 180
> movie encode /home/paloha/Desktop/movie4.mp4
Movie saved to /home/paloha/Desktop/movie4.mp4
> hide #!10 models
> movie record
> turn y 2 180
> wait 180
> movie encode /home/paloha/Desktop/movie5.mp4
Movie saved to /home/paloha/Desktop/movie5.mp4
> volume sel style surface
> surface dust #13 size 8.5
> movie record
> turn y 2 180
> wait 180
> movie encode /home/paloha/Desktop/movie6.mp4
Movie saved to /home/paloha/Desktop/movie6.mp4
> show #!10 models
> movie record
> turn y 2 180
> wait 180
> movie encode /home/paloha/Desktop/movie7.mp4
Movie saved to /home/paloha/Desktop/movie7.mp4
> save /home/paloha/.pit/Nucleosome_Chlamy_H2Blong/Pavol/NL-
> refine_3.31A_nucleosome_session.cxs
——— End of log from Tue Apr 1 09:44:49 2025 ———
opened ChimeraX session
> show #!11 models
> hide #!11 models
> volume gaussian #13 sDev 2
Opened cryosparc_P12_J276_006_volume_map.mrc x flip gaussian as #1, grid size
256,256,256, pixel 0.85, shown at step 1, values float32
> show #!13 models
> show #!11 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> hide #!11 models
> hide #!13 models
> hide #!1 models
> show #!1 models
> volume #11 level 0.06284
> undo
> volume #1 level 0.04444
> show #!13 models
> show #!10 models
> hide #!11 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.07267
> hide #!13 models
> volume #1 level 0.03298
> ui tool show Segmentations
> ui view fourup
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "/usr/lib/ucsf-chimerax/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: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "/usr/lib/ucsf-chimerax/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: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "/usr/lib/ucsf-chimerax/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: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "/usr/lib/ucsf-chimerax/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: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "/usr/lib/ucsf-chimerax/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: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File "/usr/lib/ucsf-chimerax/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: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1072, in event
self.enterEvent()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1096, in enterEvent
self.resize3DSegmentationCursor()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1202, in
resize3DSegmentationCursor
psize = self.view.pixel_size()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 1084, in pixel_size
return self.camera.view_width(p) / self.window_size[0]
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
ZeroDivisionError: division by zero
ZeroDivisionError: division by zero
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 1084, in pixel_size
return self.camera.view_width(p) / self.window_size[0]
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 24.2.8-1ubuntu1~24.04.1
OpenGL renderer: Mesa Intel(R) Graphics (MTL)
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:3
DISPLAY=:2
Manufacturer: LENOVO
Model: 21KCCTO1WW
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 14 Intel(R) Core(TM) Ultra 7 155U
Cache Size: 12288 KB
Memory:
total used free shared buff/cache available
Mem: 30Gi 15Gi 2.9Gi 4.2Gi 16Gi 15Gi
Swap: 8.0Gi 0B 8.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation Meteor Lake-P [Intel Graphics] [8086:7d45] (rev 08)
Subsystem: Lenovo Meteor Lake-P [Intel Graphics] [17aa:231e]
Kernel driver in use: i915
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
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: 2024.8.30
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-LinuxSupport: 1.0.1
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
distro: 1.9.0
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 → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'ArrayGridData' object has no attribute 'dicom_data' |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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