Opened 2 months ago

Closed 6 weeks ago

#18668 closed defect (fixed)

'NoneType' object has no attribute 'image_colors'

Reported by: chimerax-bug-report@… 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:        macOS-15.5-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/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-6/cryosparc_P245_J310_001_volume_map_sharp.mrc"

Opened cryosparc_P245_J310_001_volume_map_sharp.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.445, step 1, values float32  

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific
> mAbs/Structure/250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb"

Chain information for 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb
#2  
---  
Chain | Description  
A B C | No description available  
D F H | No description available  
E G I | No description available  
  

> set bgColor white

> graphics silhouettes true

> select add #2

38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 2 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.048514,0.99789,-0.043063,-12.015,0.99332,-0.052721,-0.10264,39.274,-0.1047,-0.037796,-0.99379,358.89

> view matrix models
> #2,-0.97101,0.18411,-0.15247,340.48,0.22723,0.90894,-0.34957,35.262,0.074233,-0.37408,-0.92442,378.92

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-6/cryosparc_P245_J310_001_volume_map_sharp_flip.mrc"

Opened cryosparc_P245_J310_001_volume_map_sharp_flip.mrc as #3, grid size
180,180,180, pixel 2.16, shown at level 0.445, step 1, values float32  

> hide #!1 models

> select add #3

38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 4 models selected  

> view matrix models
> #2,-0.52524,0.75889,0.38499,75.513,-0.29026,0.26552,-0.91937,331.23,-0.79992,-0.59464,0.080813,436.18,#3,0.59102,0.43585,-0.67877,116.11,0.47091,0.49677,0.72902,-122.86,0.65493,-0.7505,0.088355,206.17

> show sel cartoons

> hide sel atoms

> select subtract #3

38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 2 models selected  

> view matrix models
> #2,-0.79175,0.61082,0.0056473,214.3,0.3916,0.51465,-0.76274,136.64,-0.46881,-0.60169,-0.64668,500.15

> view matrix models
> #2,-0.16279,0.98643,-0.021361,35.847,0.71536,0.13291,0.686,-90.618,0.67953,0.096392,-0.72729,177.23

> view matrix models
> #2,-0.77895,0.41221,-0.47258,329.52,-0.4987,-0.86408,0.068303,417.23,-0.38019,0.28888,0.87864,60.971

> view matrix models
> #2,-0.3499,-0.15375,-0.92408,435.82,0.073829,-0.9879,0.13641,327.5,-0.93387,-0.020493,0.35702,305.14

> select up

38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 2 models selected  

> select up

38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 6 models selected  

> fitmap #2 inMap #3

Fit molecule 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb (#2) to
map cryosparc_P245_J310_001_volume_map_sharp_flip.mrc (#3) using 38337 atoms  
average map value = 0.5922, steps = 256  
shifted from previous position = 29.9  
rotated from previous position = 71.2 degrees  
atoms outside contour = 9318, contour level = 0.4447  
  
Position of 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb (#2)
relative to cryosparc_P245_J310_001_volume_map_sharp_flip.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.18767014 -0.98223204 0.00037940 336.72159587  
0.98223209 0.18767006 -0.00025793 -15.19507545  
0.00018215 0.00042106 0.99999989 28.50122976  
Axis 0.00034564 0.00010041 0.99999994  
Axis point 177.54420429 195.96922119 0.00000000  
Rotation angle (degrees) 79.18315805  
Shift along axis 28.61608687  
  

> transparency sel & #3.1 50

> volume #3 level 0.3782

> select #2/d-i

10449 atoms, 10581 bonds, 690 residues, 1 model selected  

> select #2/d-i

10449 atoms, 10581 bonds, 690 residues, 1 model selected  

> color sel black

> select #2/a-c

27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected  

> color sel black

> select #2/a-c

27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected  

> color sel gray

> color zone #3 near #2 distance 10

> select add #2

38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 2 models selected  

> select subtract #2

Nothing selected  

> ui tool show "Color Zone"

> color zone #3 near #2 distance 2.16

[Repeated 1 time(s)]

> ui tool show "Segment Map"

Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.378206  
Showing 16 region surfaces  
26 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 16 regions, 16
surfaces  

> hide #!2 models

Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.378206  
Only showing 3 of 16 regions.  
Showing 3 of 16 region surfaces  
26 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 16 regions, 3
surfaces  

> hide #!3 models

> show #!3 models

> hide #!3 models

> undo

[Repeated 4 time(s)]Smoothing and grouping, standard deviation 5 voxels  
Only showing 3 of 10 regions.  
Showing 3 of 10 region surfaces  
Got 10 regions after smoothing 5 voxels.  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> hide #!3 models

> volume #1 level 0.5125

> close

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-6/cryosparc_P245_J310_001_volume_map_sharp_flip.mrc" format mrc

Opened cryosparc_P245_J310_001_volume_map_sharp_flip.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.445, step 1, values float32  

> 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.  
  

> segmentations create #1

Opened segmentation 1 of cryosparc_P245_J310_001_volume_map_sharp_flip.mrc as
#5, grid size 180,180,180, pixel 2.16, shown at level 0.501, step 1, values
float64  

> close #5

> close

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-6/cryosparc_P245_J310_001_volume_map_sharp_flip.mrc" format mrc

Opened cryosparc_P245_J310_001_volume_map_sharp_flip.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.445, step 1, values float32  

> ui tool show "Segment Map"

No segmentation chosen  
Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.444701  
Only showing 3 of 16 regions.  
Showing 3 of 16 region surfaces  
26 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 16 regions, 3
surfaces  
Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.444701  
Only showing 10 of 16 regions.  
Showing 10 of 16 region surfaces  
26 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 16 regions, 10
surfaces  
Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.444701  
Only showing 10 of 16 regions.  
Showing 10 of 16 region surfaces  
26 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 16 regions, 10
surfaces  
Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.444701  
Showing 16 region surfaces  
26 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 16 regions, 16
surfaces  

> volume #1 level 0.3687

Ungrouped to 14 regions  
Smoothing and grouping, standard deviation 3 voxels  
Showing 16 region surfaces  
Got 16 regions after smoothing 3 voxels.  
Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.368710  
Showing 16 region surfaces  
26 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 16 regions, 16
surfaces  

> volume #1 level 0.22

Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.220032  
Showing 22 region surfaces  
37 watershed regions, grouped to 22 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 22 regions, 22
surfaces  
Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.220032  
Showing 22 region surfaces  
37 watershed regions, grouped to 22 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 22 regions, 22
surfaces  

> volume #1 level 0.2464

> volume #1 level 0.2892

> volume #1 level 0.3847

> close

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-6/cryosparc_P245_J310_001_volume_map_sharp.mrc" format mrc

Opened cryosparc_P245_J310_001_volume_map_sharp.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.445, step 1, values float32  

> close

> open /Users/kjyeol/Downloads/cryosparc_P245_J367_004_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P245_J367_004_volume_map_sharp.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.418, step 1, values float32  
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 2178, in mouseMoveEvent  
self._drag(event)  
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 2182, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb  
cb(m)  
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 1889, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
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 750, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
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 750, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
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/map/volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
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 2182, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb  
cb(m)  
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 1889, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
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 750, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
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 750, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Volume Viewer"

> volume #1 level 0.2468

> surface dust #1 size 21.6

> ui tool show "Segment Map"

Segmenting cryosparc_P245_J367_004_volume_map_sharp.mrc, density threshold
0.246827  
Only showing 22 of 35 regions.  
Showing 22 of 35 region surfaces  
52 watershed regions, grouped to 35 regions  
Showing cryosparc_P245_J367_004_volume_map_sharp.seg - 35 regions, 22 surfaces  
Smoothing and grouping, standard deviation 5 voxels  
Only showing 22 of 26 regions.  
Showing 22 of 26 region surfaces  
Got 26 regions after smoothing 5 voxels.  
Ungrouped to 16 regions, but did not show all surfaces, see Options  
Smoothing and grouping, standard deviation 5 voxels  
Only showing 22 of 26 regions.  
Showing 22 of 26 region surfaces  
Got 26 regions after smoothing 5 voxels.  
Ungrouped to 16 regions, but did not show all surfaces, see Options  

> close

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-6/cryosparc_P245_J310_001_volume_map_sharp_flip.mrc" format mrc

Opened cryosparc_P245_J310_001_volume_map_sharp_flip.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.445, step 1, values float32  
Segmenting cryosparc_P245_J310_001_volume_map_sharp_flip.mrc, density
threshold 0.444701  
Showing 16 region surfaces  
26 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J310_001_volume_map_sharp_flip.seg - 16 regions, 16
surfaces  

> close

> open /Users/kjyeol/Downloads/cryosparc_P245_J367_004_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P245_J367_004_volume_map_sharp.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.418, step 1, values float32  

> volume #1 level 0.2346

Segmenting cryosparc_P245_J367_004_volume_map_sharp.mrc, density threshold
0.234590  
Only showing 16 of 41 regions.  
Showing 16 of 41 region surfaces  
59 watershed regions, grouped to 41 regions  
Showing cryosparc_P245_J367_004_volume_map_sharp.seg - 41 regions, 16 surfaces  
Segmenting cryosparc_P245_J367_004_volume_map_sharp.mrc, density threshold
0.234590  
Only showing 20 of 41 regions.  
Showing 20 of 41 region surfaces  
59 watershed regions, grouped to 41 regions  
Showing cryosparc_P245_J367_004_volume_map_sharp.seg - 41 regions, 20 surfaces  

> close

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-6/cryosparc_P245_J310_001_volume_map_sharp_flip.mrc" format mrc

Opened cryosparc_P245_J310_001_volume_map_sharp_flip.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.445, step 1, values float32  

> close

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-5/cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc" format mrc

Opened cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc as #1, grid
size 180,180,180, pixel 2.16, shown at level 0.45, step 1, values float32  

> volume #1 level 0.3174

Segmenting cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc, density
threshold 0.317360  
Showing 16 region surfaces  
37 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.seg - 16 regions,
16 surfaces  

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> hide #2.1 models

> hide #2.3 models

> hide #2.4 models

> show #2.4 models

Segmenting cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc, density
threshold 0.317360  
Showing 16 region surfaces  
37 watershed regions, grouped to 16 regions  
Showing cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.seg - 16 regions,
16 surfaces  
Segmenting cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc, density
threshold 0.317360  
Showing 31 region surfaces  
37 watershed regions, grouped to 31 regions  
Showing cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.seg - 31 regions,
31 surfaces  
Smoothing and grouping, standard deviation 2 voxels  
Showing 24 region surfaces  
Got 24 regions after smoothing 2 voxels.  
Segmenting cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc, density
threshold 0.317360  
Showing 24 region surfaces  
37 watershed regions, grouped to 24 regions  
Showing cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.seg - 24 regions,
24 surfaces  

> close

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-6/cryosparc_P245_J310_001_volume_map_sharp.mrc" format mrc

Opened cryosparc_P245_J310_001_volume_map_sharp.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.445, step 1, values float32  

> close

> open /Users/kjyeol/Downloads/cryosparc_P245_J367_004_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P245_J367_004_volume_map_sharp.mrc as #1, grid size
180,180,180, pixel 2.16, shown at level 0.418, step 1, values float32  

> close

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/nsEM/HSV2 G3
> mAb/3-5/cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc" format mrc

Opened cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc as #1, grid
size 180,180,180, pixel 2.16, shown at level 0.45, step 1, values float32  

> volume #1 level 0.3264

> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific
> mAbs/Structure/250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb"

Chain information for 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb
#2  
---  
Chain | Description  
A B C | No description available  
D F H | No description available  
E G I | No description available  
  

> select add #2

38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> fitmap #2 inMap #1

Fit molecule 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb (#2) to
map cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc (#1) using 38337
atoms  
average map value = 0.4156, steps = 116  
shifted from previous position = 21.8  
rotated from previous position = 5.49 degrees  
atoms outside contour = 12158, contour level = 0.32639  
  
Position of 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb (#2)
relative to cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99542110 -0.09558428 -0.00069777 33.30195526  
0.09558394 0.99542124 -0.00051079 -1.02603368  
0.00074340 0.00044175 0.99999963 3.60382277  
Axis 0.00498253 -0.00753843 0.99995917  
Axis point 27.05455179 346.91117002 0.00000000  
Rotation angle (degrees) 5.48516435  
Shift along axis 3.77733845  
  

> view matrix models
> #2,0.85476,-0.51895,-0.0087465,139.83,-0.49483,-0.81988,0.28798,399.54,-0.15662,-0.24183,-0.9576,404.44

> fitmap #2 inMap #1

Fit molecule 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb (#2) to
map cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc (#1) using 38337
atoms  
average map value = 0.5491, steps = 208  
shifted from previous position = 37.5  
rotated from previous position = 53.9 degrees  
atoms outside contour = 4213, contour level = 0.32639  
  
Position of 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb (#2)
relative to cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.93812690 0.34629106 -0.00065163 -35.61140152  
0.34629122 -0.93812705 0.00014736 300.40847471  
-0.00056028 -0.00036390 -0.99999978 371.53261564  
Axis -0.98441019 -0.17588771 0.00030743  
Axis point 0.00000000 153.41014106 185.74114062  
Rotation angle (degrees) 179.98512137  
Shift along axis -17.66771203  
  

> transparency 50

> ui mousemode right select

> select clear

> ui tool show "Color Zone"

Need to color zone map before it can be split  

> color zone #1 near #2 distance 12.96

> color zone #1 near #2 distance 13.44

> color zone #1 near #2 distance 8.4

> color zone #1 near #2 distance 8.54

> color zone #1 near #2 distance 163.33

> color zone #1 near #2 distance 16.7

> color zone #1 near #2 distance 25.4

> color zone #1 near #2 distance 16.29

> color zone #1 near #2 distance 10.45

> color zone #1 near #2 distance 73.04

> color zone #1 near #2 distance 51.81

> select #2/a-c

27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected  

> transparency 0

> transparency 50

> color (#!2 & sel) #a9a9a9ff

> color zone #1 near #2 distance 10.1

> select #2/d-e

3483 atoms, 3527 bonds, 230 residues, 1 model selected  

> select #2/d-i

10449 atoms, 10581 bonds, 690 residues, 1 model selected  

> color sel #212121ff

> color zone #1 near #2 distance 10.1

> color zone #1 near #2 distance 10.02

> color zone #1 near #2 distance 5.67

[Repeated 1 time(s)]

> color zone #1 near #2 distance 5.76

> color zone #1 near #2 distance 9.68

> color zone #1 near #2 distance 9.6

> color zone #1 near #2 distance 10.62

> color zone #1 near #2 distance 10.71

> color zone #1 near #2 distance 15.62

> color zone #1 near #2 distance 15.75

> color zone #1 near #2 distance 21.48

> color zone #1 near #2 distance 21.3

> color zone #1 near #2 distance 24.78

> color zone #1 near #2 distance 24.15

> color zone #1 near #2 distance 28.33

> color zone #1 near #2 distance 28.57

> color zone #1 near #2 distance 34.35

> color sel #424242ff

> color zone #1 near #2 distance 34.35

> hide #!1 models

> show #!1 models

> hide #!2 models

> select add #2

38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 2 models selected  

> select subtract #2

Nothing selected  

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

Need to color zone map before it can be split  

> select add #2.1

9 pseudobonds, 1 model selected  

> select subtract #2.1

Nothing selected  

> show #!2 models

> hide #!2 models

> hide #2.1 models

Need to color zone map before it can be split  

> color zone #1 near #2 distance 34.35

> volume splitbyzone #1

Opened cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc 0 as #3.1, grid
size 180,180,180, pixel 2.16, shown at level 0.326, step 1, values float32  
Opened cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc 1 as #3.2, grid
size 180,180,180, pixel 2.16, shown at level 0.326, step 1, values float32  
Opened cryosparc_P245_J213_001_volume_map_sharp.mrc z flip.mrc 2 as #3.3, grid
size 180,180,180, pixel 2.16, shown at level 0.326, step 1, values float32  

> volume #3.2 level 0.08644




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple

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: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGN63KH/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 2 hours, 34 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LF27T35:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Television: Yes


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
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    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-Clipper: 0.24.0
    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-ISOLDE: 1.9
    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-QScore: 1.2
    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
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    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: 3.10.1
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    narwhals: 1.35.0
    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: 2.2.5
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    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
    platformdirs: 4.2.2
    plotly: 6.0.1
    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
    pyKVFinder: 0.7.3
    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
    toml: 0.10.2
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    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: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (3)

comment:1 by Eric Pettersen, 2 months ago

Component: Unassigned → DICOM
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → 'NoneType' object has no attribute 'image_colors'

Possibly due to earlier "'MRCGrid' object has no attribute 'dicom_data'"?

comment:2 by Zach Pearson, 6 weeks ago

For the first traceback, use the daily build. For the second, same fix as #18854.

comment:3 by Zach Pearson, 6 weeks ago

Resolution: → fixed
Status: assigned → closed
Note: See TracTickets for help on using tickets.