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Opened 2 days ago
Closed 2 days ago
#19246 closed defect (duplicate)
Orthoplanes: 'NoneType' object has no attribute 'image_colors'
| 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: macOS-15.4.1-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 0345 format ccp4 fromDatabase emdb
Opened emdb 0345 as #1, grid size 256,256,256, pixel 1.06, shown at level
0.04, step 1, values float32, fit PDB 6n51
> close session
> open 0345 format ccp4 fromDatabase emdb
Opened emdb 0345 as #1, grid size 256,256,256, pixel 1.06, shown at level
0.04, step 1, values float32, fit PDB 6n51
> close session
> open 0346 format ccp4 fromDatabase emdb
Opened emdb 0346 as #1, grid size 256,256,256, pixel 1.06, shown at level
0.031, step 1, values float32, fit PDB 6n52
> close session
> open
> /Users/grahamroseman/Downloads/cryosparc_P4_J60_class_01_00080_volume_sharp.mrc
> format mrc
Opened cryosparc_P4_J60_class_01_00080_volume_sharp.mrc as #1, grid size
360,360,360, pixel 1.07, shown at level 0.0976, step 2, values float32
> close session
> open 0345 format ccp4 fromDatabase emdb
Opened emdb 0345 as #1, grid size 256,256,256, pixel 1.06, shown at level
0.04, step 1, values float32, fit PDB 6n51
> volume #1 level 0.0364
> open 5N51 fromDatabase pdb format mmcif
Summary of feedback from opening 5N51 fetched from pdb
---
notes | Fetching compressed mmCIF 5n51 from http://files.rcsb.org/download/5n51.cif
Fetching CCD 8N8 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/8/8N8/8N8.cif
5n51 title:
Crystal structure of human Pim-1 kinase in complex with a consensus peptide
and fragment like molecule 3,4-Dibromothiophene-2-carboxylic acid [more
info...]
Chain information for 5n51 #2
---
Chain | Description | UniProt
A | Serine/threonine-protein kinase pim-1 | PIM1_HUMAN 1-313
B | Pimtide |
Non-standard residues in 5n51 #2
---
8N8 — 3,4-bis(bromanyl)thiophene-2-carboxylic acid
34 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #2
> open 6N51 fromDatabase pdb format mmcif
6n51 title:
Metabotropic Glutamate Receptor 5 bound to L-quisqualate and Nb43 [more
info...]
Chain information for 6n51 #2
---
Chain | Description | UniProt
A B | Metabotropic glutamate receptor 5 | GRM5_HUMAN 23-826
C D | Nanobody 43 |
Non-standard residues in 6n51 #2
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
QUS — (S)-2-amino-3-(3,5-dioxo-[1,2,4]oxadiazolidin-2-yl)-propionic acid
(quisqualate)
> hide #!2 models
> show #!2 models
> select /C:82
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select /C/D
1870 atoms, 1916 bonds, 246 residues, 1 model selected
> color sel yellow
> select clear
> show #!1 models
> color #1 #b2b2b272 models
> ui tool show Segmentations
Created segmentation sphere cursor with ID #3
Created segmentation sphere cursor with ID #4
Created segmentation sphere cursor with ID #5
> ui view fourup
> lighting simple
> set bgColor white
[Repeated 1 time(s)]
> close session
> open 6N51 format mmcif fromDatabase pdb
6n51 title:
Metabotropic Glutamate Receptor 5 bound to L-quisqualate and Nb43 [more
info...]
Chain information for 6n51 #1
---
Chain | Description | UniProt
A B | Metabotropic glutamate receptor 5 | GRM5_HUMAN 23-826
C D | Nanobody 43 |
Non-standard residues in 6n51 #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
QUS — (S)-2-amino-3-(3,5-dioxo-[1,2,4]oxadiazolidin-2-yl)-propionic acid
(quisqualate)
> open 0345 format ccp4 fromDatabase emdb
Opened emdb 0345 as #2, grid size 256,256,256, pixel 1.06, shown at level
0.04, step 1, values float32, fit PDB 6n51
> select /C/D
1870 atoms, 1916 bonds, 246 residues, 1 model selected
> color sel yellow
> volume #2 color #b2b2b26c
> volume #2 color #9437ff
> volume #2 color #9437ff3f
> volume #2 color #9437ff40
> select clear
> ui tool show "Segment Map"
Segmenting emdb 0345, density threshold 0.040000
Only showing 60 of 85 regions.
Showing 60 of 85 region surfaces
1916 watershed regions, grouped to 85 regions
Showing emdb 0345.seg - 85 regions, 60 surfaces
> select #3.1
1 model selected
> select #3.6
1 model selected
> select #3.2
1 model selected
> select add #3.1
2 models selected
> select add #3.6
3 models selected
> select add #3.5
4 models selected
Saving 60 regions to mrc file...
Opened 6N51noNano.mrc as #4, grid size 87,97,180, pixel 1.06, shown at step 1,
values float32
Wrote 6N51noNano.mrc
> volume resample #4 onGrid #2
Opened 6N51noNano.mrc resampled as #5, grid size 256,256,256, pixel 1.06,
shown at step 1, values float32
> volume #5 level 0.1057
> select clear
> close #5
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, 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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, 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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, 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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
Drag select of 2746, 2743, 2737, 2724, 2727, 2726, 2748, 2747, 2739, 2728,
2725, 2723, 2751, 2750, 2611, 2610, 2736, 2735, 2740, 2738, 2712, 2711, 2697,
2695, 2745, 2744, 2657, 2656, 2638, 2637, 2730, 2729, 2753, 2752, 2613, 2612,
2356, 2359, 2758, 2759, 2717, 2716, 2757, 2754, 2639, 6577 of 6592 triangles,
2636, 2653, 2651, 2448, 2749, 2722, 8528 of 8628 triangles, 2449, 2317, 2319,
2641, 2640
> select clear
Drag select of 2746, 2743, 2737, 2724, 2727, 2726, 2748, 2747, 2739, 2728,
2725, 2723, 2751, 2750, 2611, 2610, 2736, 2735, 2740, 2738, 2712, 2711, 2697,
2695, 2745, 2744, 2657, 2656, 2638, 2637, 2730, 2729, 2753, 2752, 2613, 2612,
2356, 2359, 2758, 2759, 2717, 2716, 2757, 2754, 2639, 2636, 2653, 2651, 2448,
2749, 2722, 2449, 2317, 2319, 2641, 2640
Saving 56 regions to mrc file...
Opened 6N51noNano.mrc as #5, grid size 87,97,164, pixel 1.06, shown at step 1,
values float32
Wrote 6N51noNano.mrc
> hide #!3 models
> show #!3 models
> volume resample #3 onGrid #2
> show #!5 models
> hide #!3 models
> volume #5 level 0.04312
> volume #5 level 0.04022
> volume resample #5 onGrid #2
Opened 6N51noNano.mrc resampled as #6, grid size 256,256,256, pixel 1.06,
shown at step 1, values float32
> volume #6 level 0.03986
> volume #2 level 0.02461
> close #5
> close #3-4,6
> show #!1 models
Segmenting emdb 0345, density threshold 0.024609
Only showing 60 of 161 regions.
Showing 60 of 161 region surfaces
4156 watershed regions, grouped to 161 regions
Showing emdb 0345.seg - 161 regions, 60 surfaces
> color #3 #b2b2b2b9
> color #3 #b2b2b2c3
> color #3 #b2b2b2c2
Segmenting emdb 0345, density threshold 0.024609
Only showing 60 of 161 regions.
Showing 60 of 161 region surfaces
4156 watershed regions, grouped to 161 regions
Showing emdb 0345.seg - 161 regions, 60 surfaces
> select #3.6
1 model selected
> select add #3.5
2 models selected
> select #3.12
1 model selected
> select add #3.11
2 models selected
> select #2
2 models selected
> select clear
> select #2
2 models selected
> select clear
> select #2
2 models selected
Segmenting emdb 0345, density threshold 0.024609
Only showing 80 of 161 regions.
Showing 80 of 161 region surfaces
4156 watershed regions, grouped to 161 regions
Showing emdb 0345.seg - 161 regions, 80 surfaces
> select #3.5
1 model selected
> select #3.6
1 model selected
> select add #3.5
2 models selected
> select #3.12
1 model selected
> select #3.11
1 model selected
Saving 1 regions to mrc file...
Opened 6N51noNano.mrc as #4, grid size 41,38,37, pixel 1.06, shown at step 1,
values float32
Wrote 6N51noNano.mrc
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
Drag select of 5606, 5597, 5604, 5596, 5607, 5608, 5610, 5611, 5615, 5616,
5599, 5603, 5618, 5621, 5600, 5619, 5624, 5626, 5477, 5488, 5491, 5482, 5634,
5620, 5467, 5468, 5507, 5536, 5512, 5506, 5543, 5532, 5605, 5609, 5592, 5516,
5518, 5469, 5625, 5631, 5097, 5107, 5635, 5601, 5602, 5554, 5555, 5622, 5524,
5526, 5521, 5523, 5613, 5617, 5567, 5575, 5544, 5571, 5479, 5514, 5612, 5614,
5633, 5636, 5540, 5515, 5402, 5406, 5410, 5481, 5509, 5487, 5490, 5094, 5129,
5546
Saving 76 regions to mrc file...
Opened 6N51noNano.mrc as #5, grid size 111,121,177, pixel 1.06, shown at step
1, values float32
Wrote 6N51noNano.mrc
> hide #!3 models
> volume #5 level 0.06803
> volume #5 level 0.02818
> volume resample #5 onGrid #2
Opened 6N51noNano.mrc resampled as #6, grid size 256,256,256, pixel 1.06,
shown at step 1, values float32
> save /Users/grahamroseman/Desktop/YaleDocuments/Papers/6N51noNano.mrc models
> #6
> close #2
> close #4
> close #5
> close #6
> open /Users/grahamroseman/Desktop/YaleDocuments/Papers/6N51noNano.mrc
Opened 6N51noNano.mrc as #2, grid size 256,256,256, pixel 1.06, shown at level
0.0288, step 1, values float32
> open /Users/grahamroseman/Downloads/NAM_Class1and2_NUR.mrc format mrc
Opened NAM_Class1and2_NUR.mrc as #4, grid size 360,360,360, pixel 1.07, shown
at level 0.0854, step 2, values float32
> open 0346 format ccp4 fromDatabase emdb
Opened emdb 0346 as #5, grid size 256,256,256, pixel 1.06, shown at level
0.031, step 1, values float32, fit PDB 6n52
> close #4
> open
> /Users/grahamroseman/Desktop/YaleDocuments/Papers/mGluRallostericmodulations/CarmenSAMquis_380box.mrc
> format mrc
Opened CarmenSAMquis_380box.mrc as #4, grid size 380,380,380, pixel 1.07,
shown at level 0.0729, step 2, values float32
> open
> "/Users/grahamroseman/Desktop/YaleDocuments/Papers/mGluRallostericmodulations/mGluR5allostericpapa/redo
> SAM NUR class1 of ab initio.mrc" format mrc
Opened redo SAM NUR class1 of ab initio.mrc as #6, grid size 360,360,360,
pixel 1.07, shown at level 0.0877, step 2, values float32
> volume #4 step 1
> volume #6 step 1
> select add #4
78 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3.1,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.2,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.3,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.4,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.7,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.8,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.9,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.10,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.13,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.14,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.15,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.16,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.17,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.18,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.19,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.20,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.21,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.22,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.23,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.24,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.25,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.26,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.27,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.28,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.29,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.30,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.31,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.32,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.33,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.34,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.35,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.36,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.37,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.38,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.39,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.40,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.41,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.42,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.43,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.44,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.45,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.46,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.47,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.48,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.49,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.50,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.51,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.52,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.53,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.54,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.55,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.56,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.57,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.58,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.59,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.60,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.61,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.62,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.63,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.64,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.65,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.66,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.67,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.68,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.69,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.70,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.71,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.72,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.73,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.74,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.75,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.76,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.77,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.78,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.79,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#3.80,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02,#4,1,0,0,305.55,0,1,0,64.136,0,0,1,-35.02
> view matrix models
> #3.1,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.2,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.3,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.4,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.7,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.8,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.9,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.10,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.13,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.14,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.15,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.16,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.17,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.18,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.19,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.20,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.21,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.22,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.23,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.24,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.25,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.26,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.27,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.28,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.29,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.30,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.31,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.32,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.33,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.34,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.35,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.36,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.37,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.38,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.39,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.40,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.41,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.42,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.43,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.44,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.45,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.46,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.47,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.48,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.49,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.50,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.51,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.52,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.53,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.54,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.55,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.56,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.57,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.58,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.59,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.60,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.61,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.62,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.63,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.64,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.65,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.66,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.67,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.68,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.69,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.70,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.71,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.72,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.73,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.74,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.75,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.76,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.77,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.78,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.79,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#3.80,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646,#4,1,0,0,325.52,0,1,0,-74.275,0,0,1,-69.646
> view matrix models
> 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> view matrix models
> 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> view matrix models
> 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> view matrix models
> 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97773,-0.18991,324.83,#3.52,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.53,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.54,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.55,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.56,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.57,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.58,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.59,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.60,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.61,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.62,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.63,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.64,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.65,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.66,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.67,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.68,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.69,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.70,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.71,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.72,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.73,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.74,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.75,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.76,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.77,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.78,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.79,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#3.80,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83,#4,0.84337,-0.17573,0.50779,233.11,-0.52986,-0.11478,0.84029,-109.25,-0.089377,-0.97773,-0.18991,324.83
> select subtract #4
76 models selected
> hide #!6 models
> show #!6 models
> select add #6
78 models selected
> view matrix models
> 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> view matrix models
> 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> view matrix models
> 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> view matrix models
> 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> view matrix models
> 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> view matrix models
> 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> volume #4 level 0.2911
> volume #6 level 0.2103
> volume resample #4 onGrid #2
Opened CarmenSAMquis_380box.mrc resampled as #7, grid size 256,256,256, pixel
1.06, shown at step 1, values float32
> volume resample #6 onGrid #2
Opened redo SAM NUR class1 of ab initio.mrc resampled as #8, grid size
256,256,256, pixel 1.06, shown at step 1, values float32
> close #4
> close #6
> volume #7 level 0.2091
> ui tool show "Fit in Map"
> volume #7 level 0.1669
> fitmap #7 inMap #2
Fit map CarmenSAMquis_380box.mrc resampled in map 6N51noNano.mrc using 85808
points
correlation = 0.4739, correlation about mean = 0.1461, overlap = 620.9
steps = 432, shift = 12.4, angle = 28.4 degrees
Position of CarmenSAMquis_380box.mrc resampled (#7) relative to 6N51noNano.mrc
(#2) coordinates:
Matrix rotation and translation
0.91661144 0.35931488 -0.17526061 -10.29980228
-0.39365008 0.88767585 -0.23889581 99.34288075
0.06973579 0.28796598 0.95509817 -53.68013935
Axis 0.55395864 -0.25759673 -0.79169044
Axis point 231.27161427 99.60802711 0.00000000
Rotation angle (degrees) 28.39468031
Shift along axis 11.20198703
> select add #7
78 models selected
> select add #2
80 models selected
> select add #3
85 models selected
> select subtract #2
83 models selected
> select subtract #3
2 models selected
> view matrix models
> #7,0.91661,0.35931,-0.17526,-20.149,-0.39365,0.88768,-0.2389,85.18,0.069736,0.28797,0.9551,-55.056
> view matrix models
> #7,0.48036,0.87206,-0.093564,-47.99,-0.81771,0.48388,0.31178,121.82,0.31717,-0.073259,0.94554,-34.295
> view matrix models
> #7,0.044285,-0.95713,0.28624,215.73,0.95717,0.12271,0.26223,-48.221,-0.28612,0.26237,0.92157,-1.1305
> view matrix models
> #7,0.64445,0.73722,-0.20295,-35.018,-0.73898,0.66867,0.082433,116.78,0.19648,0.096849,0.97571,-47.039
> view matrix models
> #7,0.64445,0.73722,-0.20295,-29.742,-0.73898,0.66867,0.082433,124.15,0.19648,0.096849,0.97571,-48.171
> fitmap #7 inMap #2
Fit map CarmenSAMquis_380box.mrc resampled in map 6N51noNano.mrc using 85808
points
correlation = 0.8294, correlation about mean = 0.5568, overlap = 1938
steps = 272, shift = 4.25, angle = 22.2 degrees
Position of CarmenSAMquis_380box.mrc resampled (#7) relative to 6N51noNano.mrc
(#2) coordinates:
Matrix rotation and translation
0.31688041 0.93373446 -0.16651353 -23.51158206
-0.93203267 0.33909252 0.12779424 193.35602366
0.17578938 0.11470056 0.97772280 -46.19048054
Axis -0.00690248 -0.18044883 -0.98356015
Axis point 126.23894608 117.45738091 0.00000000
Rotation angle (degrees) 71.52759602
Shift along axis 10.70253517
> volume #7 level 0.1331
> volume #2 level 0.02662
> fitmap #5 inMap #8
Fit map emdb 0346 in map redo SAM NUR class1 of ab initio.mrc resampled using
102628 points
correlation = 0.9307, correlation about mean = 0.7564, overlap = 1069
steps = 196, shift = 12.2, angle = 22 degrees
Position of emdb 0346 (#5) relative to redo SAM NUR class1 of ab initio.mrc
resampled (#8) coordinates:
Matrix rotation and translation
0.92963433 -0.33755862 0.14776397 28.06413916
0.32692223 0.94057194 0.09190362 -43.76896144
-0.17000551 -0.03712944 0.98474338 21.48251267
Axis -0.17255687 0.42495549 0.88861519
Axis point 137.71386127 52.20633825 0.00000000
Rotation angle (degrees) 21.95545287
Shift along axis -4.35283374
> volume #8 level 0.1815
> ui tool show "Measure Volume and Area"
> volume #2 level 0.02662
> volume #2 level 0.025
> volume #2 level 0.027
> volume #2 level 0.026
> volume #2 level 0.0265
> volume #2 level 0.027
> volume #2 level 0.0275
> volume #2 level 0.0268
> volume #2 level 0.0269
> volume #2 level 0.0268
> volume #2 level 0.02685
> hide #!5 models
> show #!5 models
> volume #5 level 0.02647
> volume #5 level 0.026
> volume #5 level 0.0269
> volume #5 level 0.0266
> volume #5 level 0.0265
> volume #5 level 0.0264
> volume #5 level 0.0263
> volume #5 level 0.0264
> volume #5 level 0.02645
> volume #5 level 0.0263
> volume #5 level 0.02635
> volume #5 level 0.02637
> volume #5 level 0.02633
> volume #5 level 0.02632
> volume #5 level 0.02631
> volume #5 level 0.02632
[Repeated 11 time(s)]
> volume #5 level 0.02631
> volume #7 level 0.1331
> volume #7 level 0.1325
> volume #7 level 0.1326
[Repeated 1 time(s)]
> volume #7 level 0.1325
> volume #8 level 0.1274
> volume #8 level 0.126
> volume #8 level 0.1255
> volume #8 level 0.1256
> volume #8 level 0.1257
> volume #8 level 0.1258
[Repeated 1 time(s)]
> volume #8 level 0.1257
[Repeated 2 time(s)]
> select subtract #7
Nothing selected
> show #!5 models
> fitmap #5 inMap #8
Fit map emdb 0346 in map redo SAM NUR class1 of ab initio.mrc resampled using
174189 points
correlation = 0.9303, correlation about mean = 0.773, overlap = 1290
steps = 140, shift = 0.0147, angle = 0.00164 degrees
Position of emdb 0346 (#5) relative to redo SAM NUR class1 of ab initio.mrc
resampled (#8) coordinates:
Matrix rotation and translation
0.92964321 -0.33753452 0.14776315 28.06323669
0.32690069 0.94058102 0.09188734 -43.75507102
-0.16999836 -0.03711857 0.98474503 21.46951786
Axis -0.17253178 0.42497247 0.88861194
Axis point 137.67341332 52.21690907 0.00000000
Rotation angle (degrees) 21.95395089
Shift along axis -4.35843076
> fitmap #5 inMap #8
Fit map emdb 0346 in map redo SAM NUR class1 of ab initio.mrc resampled using
174189 points
correlation = 0.9303, correlation about mean = 0.773, overlap = 1290
steps = 104, shift = 0.00878, angle = 0.0031 degrees
Position of emdb 0346 (#5) relative to redo SAM NUR class1 of ab initio.mrc
resampled (#8) coordinates:
Matrix rotation and translation
0.92963722 -0.33752817 0.14781533 28.04786234
0.32689443 0.94058441 0.09187488 -43.75638140
-0.17004315 -0.03709030 0.98473836 21.47411026
Axis -0.17247201 0.42508909 0.88856776
Axis point 137.67211607 52.17186045 0.00000000
Rotation angle (degrees) 21.95466091
Shift along axis -4.35662967
> fitmap #5 inMap #8
Fit map emdb 0346 in map redo SAM NUR class1 of ab initio.mrc resampled using
174189 points
correlation = 0.9303, correlation about mean = 0.773, overlap = 1290
steps = 104, shift = 0.0137, angle = 0.00549 degrees
Position of emdb 0346 (#5) relative to redo SAM NUR class1 of ab initio.mrc
resampled (#8) coordinates:
Matrix rotation and translation
0.92963527 -0.33754252 0.14779480 28.04993558
0.32689360 0.94057558 0.09196824 -43.77693887
-0.17005537 -0.03718375 0.98473272 21.49940328
Axis -0.17271243 0.42505483 0.88853745
Axis point 137.74488969 52.16054621 0.00000000
Rotation angle (degrees) 21.95591896
Shift along axis -4.34914714
> hide #!5 models
> hide #!8 models
> show #!7 models
> show #!2 models
> fitmap #2 inMap #7
Fit map 6N51noNano.mrc in map CarmenSAMquis_380box.mrc resampled using 196983
points
correlation = 0.7892, correlation about mean = 0.673, overlap = 2238
steps = 188, shift = 0.021, angle = 0.0222 degrees
Position of 6N51noNano.mrc (#2) relative to CarmenSAMquis_380box.mrc resampled
(#7) coordinates:
Matrix rotation and translation
0.31656818 -0.93211594 0.17591039 195.81295522
0.93380197 0.33882994 0.11492668 -38.32861200
-0.16672870 0.12788334 0.97767448 16.56532337
Axis 0.00682950 0.18060624 0.98353177
Axis point 126.25694847 117.42296007 0.00000000
Rotation angle (degrees) 71.54641616
Shift along axis 10.70743955
> fitmap #2 inMap #7
Fit map 6N51noNano.mrc in map CarmenSAMquis_380box.mrc resampled using 196983
points
correlation = 0.7892, correlation about mean = 0.673, overlap = 2238
steps = 1048, shift = 0.0151, angle = 0.0117 degrees
Position of 6N51noNano.mrc (#2) relative to CarmenSAMquis_380box.mrc resampled
(#7) coordinates:
Matrix rotation and translation
0.31657942 -0.93214984 0.17571040 195.85233066
0.93381244 0.33880539 0.11491402 -38.32304728
-0.16664871 0.12770114 0.97771193 16.57103635
Axis 0.00674017 0.18045944 0.98355933
Axis point 126.27134442 117.45295679 0.00000000
Rotation angle (degrees) 71.54568742
Shift along axis 10.70291928
> fitmap #7 inMap #2
Fit map CarmenSAMquis_380box.mrc resampled in map 6N51noNano.mrc using 184538
points
correlation = 0.8033, correlation about mean = 0.6135, overlap = 2127
steps = 2000, shift = 0.495, angle = 0.438 degrees
Position of CarmenSAMquis_380box.mrc resampled (#7) relative to 6N51noNano.mrc
(#2) coordinates:
Matrix rotation and translation
0.31820999 0.93442351 -0.15998472 -24.91137675
-0.93142366 0.33959418 0.13086545 192.52805214
0.17661363 0.10737086 0.97840642 -45.13353238
Axis -0.01239094 -0.17752041 -0.98403911
Axis point 125.15991349 117.84110987 0.00000000
Rotation angle (degrees) 71.45162019
Shift along axis 10.54417827
> fitmap #7 inMap #2
Fit map CarmenSAMquis_380box.mrc resampled in map 6N51noNano.mrc using 184538
points
correlation = 0.7973, correlation about mean = 0.606, overlap = 2091
steps = 2000, shift = 0.53, angle = 0.521 degrees
Position of CarmenSAMquis_380box.mrc resampled (#7) relative to 6N51noNano.mrc
(#2) coordinates:
Matrix rotation and translation
0.31831288 0.93391154 -0.16274564 -24.74884998
-0.92965302 0.34112165 0.13921668 190.58630354
0.18553213 0.10698251 0.97679710 -46.02057435
Axis -0.01700022 -0.18368075 -0.98283894
Axis point 124.20990037 116.97058535 0.00000000
Rotation angle (degrees) 71.45098436
Shift along axis 10.64451207
> volume #2 level 0.02566
> volume #2 level 0.0209
> volume #2 level 0.01882
> volume #2 level 0.0189
> volume #2 level 0.0191
> volume #2 level 0.0195
> volume #2 level 0.0194
> volume #2 level 0.0193
> volume #2 level 0.0192
> volume #2 level 0.01926
> volume #2 level 0.01927
> volume #5 level 0.02517
> volume #5 level 0.0251
> volume #5 level 0.0245
> volume #5 level 0.0247
> volume #5 level 0.0246
> volume #5 level 0.0247
> volume #5 level 0.02466
> volume #5 level 0.02464
> volume #5 level 0.02468
> volume #7 level 0.1256
> volume #7 level 0.125
> volume #7 level 0.124
> volume #7 level 0.1255
> volume #7 level 0.1245
> volume #7 level 0.1244
> volume #7 level 0.1243
> volume #7 level 0.1244
> volume #7 level 0.1243
[Repeated 1 time(s)]
> volume #8 level 0.1198
> volume #8 level 0.115
> volume #8 level 0.119
> volume #8 level 0.1199
> volume #8 level 0.1195
> volume #8 level 0.1193
> volume #8 level 0.1192
[Repeated 1 time(s)]
> volume #8 level 0.1193
[Repeated 1 time(s)]
> fitmap #7 inMap #2
Fit map CarmenSAMquis_380box.mrc resampled in map 6N51noNano.mrc using 224489
points
correlation = 0.7932, correlation about mean = 0.6124, overlap = 2176
steps = 2000, shift = 1.16, angle = 0.88 degrees
Position of CarmenSAMquis_380box.mrc resampled (#7) relative to 6N51noNano.mrc
(#2) coordinates:
Matrix rotation and translation
0.31891512 0.93476619 -0.15654172 -25.65544584
-0.93232293 0.33911503 0.12559836 193.90778379
0.17049076 0.10589222 0.97965287 -44.55225890
Axis -0.01039564 -0.17252042 -0.98495108
Axis point 125.67992093 118.89920107 0.00000000
Rotation angle (degrees) 71.40712120
Shift along axis 10.69544864
> fitmap #7 inMap #2
Fit map CarmenSAMquis_380box.mrc resampled in map 6N51noNano.mrc using 224489
points
correlation = 0.7961, correlation about mean = 0.617, overlap = 2189
steps = 2000, shift = 0.788, angle = 0.674 degrees
Position of CarmenSAMquis_380box.mrc resampled (#7) relative to 6N51noNano.mrc
(#2) coordinates:
Matrix rotation and translation
0.31723242 0.93367706 -0.16616481 -23.69828587
-0.93117940 0.33985965 0.13191039 192.28604512
0.17963442 0.11288300 0.97723534 -46.51145506
Axis -0.01003162 -0.18231225 -0.98318951
Axis point 125.60640136 117.11630544 0.00000000
Rotation angle (degrees) 71.50851575
Shift along axis 10.91120516
> open
> /Users/grahamroseman/Downloads/cryosparc_P3_J52_001_volume_map_sharp.mrc
Opened cryosparc_P3_J52_001_volume_map_sharp.mrc as #4, grid size 360,360,360,
pixel 1.07, shown at level 0.0843, step 2, values float32
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, 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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, 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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1931, in
moved_marker_cb
self.plane_viewer.on_color_changed()
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, 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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 754, in
on_color_changed
colors = self.view.drawing.parent.image_colors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2075.101.2.0.0 (iBridge: 22.16.14248.0.0,0)
OS Loader Version: 583~900
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 7 days, 3 hours, 42 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG UltraFine:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 2 days ago
| Component: | Unassigned → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Orthoplanes: 'NoneType' object has no attribute 'image_colors' |
comment:2 by , 2 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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