Opened 10 months ago

Closed 10 months ago

#16465 closed defect (fixed)

flip_matrix: 'NoneType' object is not subscriptable

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-49-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J20/J20_005_volume_map.mrc

Opened J20_005_volume_map.mrc as #1, grid size 256,256,256, pixel 0.772, shown
at level 0.0476, step 1, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J50/J50_004_volume_map.mrc

Opened J50_004_volume_map.mrc as #2, grid size 256,256,256, pixel 0.772, shown
at level 0.0165, step 1, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J88/J88_004_volume_map.mrc

Opened J88_004_volume_map.mrc as #3, grid size 256,256,256, pixel 0.772, shown
at level 0.0455, step 1, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J112_class*/*_volume_map.mrc

Opened J115_004_volume_map.mrc as #4.1, grid size 256,256,256, pixel 0.772,
shown at level 0.0406, step 1, values float32  
Opened J265_004_volume_map.mrc as #4.2, grid size 256,256,256, pixel 0.772,
shown at level 0.0427, step 1, values float32  
Opened J266_002_volume_map.mrc as #4.3, grid size 256,256,256, pixel 0.772,
shown at level 0.0414, step 1, values float32  
Opened J267_002_volume_map.mrc as #4.4, grid size 256,256,256, pixel 0.772,
shown at level 0.0421, step 1, values float32  
Opened J268_002_volume_map.mrc as #4.5, grid size 256,256,256, pixel 0.772,
shown at level 0.0434, step 1, values float32  
Opened J269_002_volume_map.mrc as #4.6, grid size 256,256,256, pixel 0.772,
shown at level 0.0624, step 1, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J200/J200_004_volume_map.mrc

Opened J200_004_volume_map.mrc as #5, grid size 380,380,380, pixel 0.772,
shown at level 0.00315, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J211/J211_005_volume_map.mrc

Opened J211_005_volume_map.mrc as #6, grid size 380,380,380, pixel 0.772,
shown at level 0.00185, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J211/J211_005_volume_map_deepemhancer.mrc

Opened J211_005_volume_map_deepemhancer.mrc as #7, grid size 380,380,380,
pixel 0.772, shown at level 0.000121, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J221/J221_map_locres.mrc

Opened J221_map_locres.mrc as #8, grid size 380,380,380, pixel 0.772, shown at
level 3.76, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/cryoEM_processing_pipeline/J211_viewing_direction_distribution_iteration_005.bild

Opened BILD data containing 3072 objects  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J249/J249_002_volume_map.mrc

Opened J249_002_volume_map.mrc as #10, grid size 380,380,380, pixel 0.772,
shown at level 0.00268, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J253/J253_002_volume_map.mrc

Opened J253_002_volume_map.mrc as #11, grid size 380,380,380, pixel 0.772,
shown at level 0.00245, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J257/J249_J253_combined_volume.mrc

Opened J249_J253_combined_volume.mrc as #12, grid size 380,380,380, pixel
0.772, shown at level 0.00379, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J225/J225_mask.mrc

Opened J225_mask.mrc as #13, grid size 380,380,380, pixel 0.772, shown at
level 0.258, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/J226/J226_mask.mrc

Opened J226_mask.mrc as #14, grid size 380,380,380, pixel 0.772, shown at
level 5e-05, step 2, values float32  

> open
> /biophysik/lad58072/cryoEM_projects_not_exosome/xrn1_core_tudor_apo/phenix_J211/RealSpaceRefine_46/006_refined__real_space_refined_046.pdb

Chain information for 006_refined__real_space_refined_046.pdb #15  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> lighting default

> lighting soft

> graphics silhouettes true color midnightblue

> lighting ambientColor navajowhite ambientIntensity 1.8

> cartoon style width 1.4 thickness 0.4 xsection oval

> transparency 0 cartoons

> transparency 0 surfaces

> hide models

> color #1-12 paleturquoise

> color #13-14 blueviolet

> color #15 mediumblue

> volume flip #1-4 axis z

Opened J20_005_volume_map.mrc z flip as #16, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  
Opened J50_004_volume_map.mrc z flip as #17, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  
Opened J88_004_volume_map.mrc z flip as #18, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  
Opened J115_004_volume_map.mrc z flip as #19, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  
Opened J265_004_volume_map.mrc z flip as #20, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  
Opened J266_002_volume_map.mrc z flip as #21, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  
Opened J267_002_volume_map.mrc z flip as #22, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  
Opened J268_002_volume_map.mrc z flip as #23, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  
Opened J269_002_volume_map.mrc z flip as #24, grid size 256,256,256, pixel
0.772, shown at step 1, values float32  

> close #1-4

> rename #16 id #1

> rename #17 id #2

> rename #18 id #3

> rename #19 id #4.1

> rename #20 id #4.2

> rename #21 id #4.3

> rename #22 id #4.4

> rename #23 id #4.5

> rename #24 id #4.6

> view matrix models
> #1,-0.99756,-0.069461,0.00661,252.71,-0.069576,0.99739,-0.019212,56.752,-0.0052583,-0.019625,-0.99979,246.81,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.99968,0.024608,0.005446,242.9,-0.024647,-0.99967,-0.0070544,248.59,0.0052706,-0.0071864,0.99996,48.556,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,-0.99968,0.024608,0.005446,242.9,-0.024647,-0.99967,-0.0070544,248.59,0.0052706,-0.0071864,0.99996,48.556,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,-0.99968,0.024608,0.005446,242.9,-0.024647,-0.99967,-0.0070544,248.59,0.0052706,-0.0071864,0.99996,48.556,#4.1,1,0,0,0,0,1,0,0,0,0,1,0

> volume step 1

> volume #1 level 0.08

> volume #2 level 0.04

> volume #3 level 0.08

> volume #4 level 0.10

> volume #5 level 0.12

> volume #6 level 0.07

> volume #7 level 0.24

> volume #10-12 level 0.08

> volume #13-14 level 0.9

> hide models

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) UHD Graphics (ADL-S GT1)
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:1
Manufacturer: LENOVO
Model: 21D7S83Y00
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 12th Gen Intel(R) Core(TM) i9-12950HX
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           125Gi       2.6Gi       115Gi       644Mi       7.0Gi       121Gi
	Swap:          8.0Gi          0B       8.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:4688] (rev 0c)	
	Subsystem: Lenovo Device [17aa:22fb]	
	Kernel driver in use: i915

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
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    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.23.1
    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: 1.8
    ChimeraX-CoreFormats: 1.2
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    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
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    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
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    ChimeraX-ISOLDE: 1.8
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    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
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    ChimeraX-MatchMaker: 2.1.3
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    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
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    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
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    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
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Change History (2)

comment:1 by pett, 10 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → flip_matrix: 'NoneType' object is not subscriptable

comment:2 by Tom Goddard, 10 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Flipped volume matrix() routine did not properly handle the case when from_cache_only = True and there is no cached matrix so None is returned.

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