Opened 23 months ago

Closed 22 months ago

#10349 closed defect (duplicate)

Segger: fmap.data is None

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

Description 

The following bug report has been submitted:
Platform:        macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/rslack/Downloads/5j2m.pdb format pdb

Summary of feedback from opening /Users/rslack/Downloads/5j2m.pdb  
---  
warning | Cannot find LINK/SSBOND atom SG in residue MRG /P:817  
  
5j2m.pdb title:  
Hiv-1 reverse transcriptase In complex with DNA and EFDA-triphosphate, A
translocation-defective RT inhibitor [more info...]  
  
Chain information for 5j2m.pdb #1  
---  
Chain | Description | UniProt  
A | PR160GAG-POL | POL_HV1H2 1-560  
B | PR160GAG-POL | POL_HV1H2 1-440  
P | DNA (5'- D(*ap*CP*ap*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)
P*CP*GP*CP*CP*G)-3') |  
T | DNA (27-mer) |  
  
Non-standard residues in 5j2m.pdb #1  
---  
6FN — 2'-deoxy-4'-ethynyl-2-fluoroadenosine
5'-(tetrahydrogentriphosphate)  
MG — magnesium ion  
MRG — N2-(3-mercaptopropyl)-2'-deoxyguanosine-5'-monophosphate  
  

> open "/Users/rslack/Library/CloudStorage/OneDrive-
> EmoryUniversity/Documents/Data/3D
> Maps/cryosparc_P11_J21_004_volume_map_sharp.mrc"

Opened cryosparc_P11_J21_004_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.84, shown at level 0.0658, step 1, values float32  

> ui tool show "Segment Map"

Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold
0.065843  
Showing 48 region surfaces  
1150 watershed regions, grouped to 48 regions  
Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 48 regions, 48 surfaces  

> ui tool show "Fit to Segments"

> select #1:P,T #3

49 models selected  

> ui tool show "Fit to Segments"

Simulating map res 4.000, grid 2.000  

> molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 5j2m.pdb map 4 as #4, grid size 45,59,70, pixel 2, shown at level
0.103, step 1, values float32  
Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size
256,256,256, pixel 0.84, shown at step 1, values float32  
Top score: 0.54351, z-score: 17.45630 (avg: 0.4723, stdev: 0.0041)  
Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size
256,256,256, pixel 0.84, shown at step 1, values float32  
Top score: 0.54351, z-score: 17.45630 (avg: 0.4723, stdev: 0.0041)  
Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size
256,256,256, pixel 0.84, shown at step 1, values float32  
Generating Laplace version of cryosparc_P11_J21_004_volume_map_sharp.mrc  
Opened cryosparc_P11_J21_004_volume_map_sharp.mrc Laplacian as #6, grid size
256,256,256, pixel 0.84, shown at step 1, values float32  
Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size
256,256,256, pixel 0.84, shown at step 1, values float32  
Top score: 0.54351, z-score: 17.45630 (avg: 0.4723, stdev: 0.0041)  

> show #!4 models

> select subtract #3

Nothing selected  

> hide #!6 models

> hide #!4 models

> hide #!3 models

> hide #!1 models

> close #4

> show #!6 models

> close #6

> show #!3 models

> show #!1 models

> volume #2 level 0.4721

> volume #2 level 0.09354

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2571, in
FitMapToRegionsAroundSel  
self.FitMapToGroupsAround ( fmap, smod, regs, dmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2485, in FitMapToGroupsAround  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> select #1:P,T #3

49 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2571, in
FitMapToRegionsAroundSel  
self.FitMapToGroupsAround ( fmap, smod, regs, dmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2485, in FitMapToGroupsAround  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2571, in
FitMapToRegionsAroundSel  
self.FitMapToGroupsAround ( fmap, smod, regs, dmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2485, in FitMapToGroupsAround  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> hide #!2 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2571, in
FitMapToRegionsAroundSel  
self.FitMapToGroupsAround ( fmap, smod, regs, dmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2485, in FitMapToGroupsAround  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Simulating map res 4.000, grid 2.000  

> molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 5j2m.pdb map 4 as #4, grid size 45,59,70, pixel 2, shown at level
0.103, step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2571, in
FitMapToRegionsAroundSel  
self.FitMapToGroupsAround ( fmap, smod, regs, dmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2485, in FitMapToGroupsAround  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2571, in
FitMapToRegionsAroundSel  
self.FitMapToGroupsAround ( fmap, smod, regs, dmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2485, in FitMapToGroupsAround  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> ui tool show "Fit to Segments"

Simulating map res 4.000, grid 2.000  

> molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 5j2m.pdb map 4 as #5, grid size 45,59,70, pixel 2, shown at level
0.103, step 1, values float32  
Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #6, grid size
256,256,256, pixel 0.84, shown at step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1856, in FitToEachRegion  
self.saFitMapToPoints ( fmap, tpoints, to_map )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1894, in saFitMapToPoints  
fpoints, fpoint_weights = fit_points(fmap)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 5187, in fit_points  
mat = fmap.data.full_matrix()  
AttributeError: 'NoneType' object has no attribute 'full_matrix'  
  
AttributeError: 'NoneType' object has no attribute 'full_matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 5187, in fit_points  
mat = fmap.data.full_matrix()  
  
See log for complete Python traceback.  
  
Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #7, grid size
256,256,256, pixel 0.84, shown at step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1856, in FitToEachRegion  
self.saFitMapToPoints ( fmap, tpoints, to_map )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1894, in saFitMapToPoints  
fpoints, fpoint_weights = fit_points(fmap)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 5187, in fit_points  
mat = fmap.data.full_matrix()  
AttributeError: 'NoneType' object has no attribute 'full_matrix'  
  
AttributeError: 'NoneType' object has no attribute 'full_matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 5187, in fit_points  
mat = fmap.data.full_matrix()  
  
See log for complete Python traceback.  
  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> ui tool show "Fit in Map"

> hide #!7 models

> hide #!6 models

> show #!6 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> select add #6

51 models selected  

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select subtract #6

49 models selected  

> select subtract #3

Nothing selected  

> fitmap #1 inMap #2

Fit molecule 5j2m.pdb (#1) to map cryosparc_P11_J21_004_volume_map_sharp.mrc
(#2) using 9107 atoms  
average map value = 0.06842, steps = 368  
shifted from previous position = 0.174  
rotated from previous position = 4.12 degrees  
atoms outside contour = 6316, contour level = 0.093545  
  
Position of 5j2m.pdb (#1) relative to
cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.90579566 -0.42349283 0.01371294 108.24317464  
-0.42283294 -0.90552390 -0.03519623 109.21757910  
0.02732274 0.02608231 -0.99928634 107.86680013  
Axis 0.97615891 -0.21680238 0.01051207  
Axis point 0.00000000 65.76877451 54.37363323  
Rotation angle (degrees) 178.20132833  
Shift along axis 83.11781112  
  

> fitmap #1 inMap #2

Fit molecule 5j2m.pdb (#1) to map cryosparc_P11_J21_004_volume_map_sharp.mrc
(#2) using 9107 atoms  
average map value = 0.06842, steps = 48  
shifted from previous position = 0.00316  
rotated from previous position = 0.0129 degrees  
atoms outside contour = 6321, contour level = 0.093545  
  
Position of 5j2m.pdb (#1) relative to
cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.90589116 -0.42328889 0.01370113 108.24541315  
-0.42262906 -0.90561864 -0.03520733 109.21576377  
0.02731086 0.02610351 -0.99928611 107.86550289  
Axis 0.97618337 -0.21669254 0.01050574  
Axis point 0.00000000 65.76132119 54.37376691  
Rotation angle (degrees) 178.20042523  
Shift along axis 83.13433797  
  

> volume #2 color #b2b2b264

> volume #2 color #b2b2b263

> volume #2 level 0.1585

> hide #!1 models

> show #!1 models

> volume #2 level 0.09671

> show #!3 models

> hide #!2 models

Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold
0.096714  
Showing 43 region surfaces  
686 watershed regions, grouped to 43 regions  
Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 43 regions, 43 surfaces  

> undo

[Repeated 1 time(s)]

> close #7

> close #6

Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold
0.096714  
Only showing 60 of 161 regions.  
Showing 60 of 161 region surfaces  
686 watershed regions, grouped to 161 regions  
Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 161 regions, 60 surfaces  
Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold
0.096714  
Only showing 60 of 177 regions.  
Showing 60 of 177 region surfaces  
686 watershed regions, grouped to 177 regions  
Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 177 regions, 60 surfaces  
Segmenting cryosparc_P11_J21_004_volume_map_sharp.mrc, density threshold
0.096714  
Only showing 60 of 220 regions.  
Showing 60 of 220 region surfaces  
686 watershed regions, grouped to 220 regions  
Showing cryosparc_P11_J21_004_volume_map_sharp.seg - 220 regions, 60 surfaces  
Please select one or more regions to align the structure to  

> select #1:P,T #3

61 models selected  

> show #!5 models

> hide #!5 models

> select #1:P,T #3

61 models selected  

> fitmap #1 inMap #2

Fit molecule 5j2m.pdb (#1) to map cryosparc_P11_J21_004_volume_map_sharp.mrc
(#2) using 9107 atoms  
average map value = 0.06842, steps = 48  
shifted from previous position = 0.0196  
rotated from previous position = 0.00826 degrees  
atoms outside contour = 6496, contour level = 0.096714  
  
Position of 5j2m.pdb (#1) relative to
cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.90583612 -0.42340809 0.01365693 108.23291295  
-0.42275042 -0.90556348 -0.03516901 109.22922796  
0.02725806 0.02608389 -0.99928806 107.87222570  
Axis 0.97616928 -0.21675719 0.01048104  
Axis point 0.00000000 65.77113954 54.37772399  
Rotation angle (degrees) 178.20210042  
Shift along axis 83.10803736  
  
Opened 5j2m.pdb map 3 as #4, grid size 83,111,134, pixel 1, shown at level
0.11, step 1, values float32  

> fitmap #1 inMap #2 resolution 3 metric correlation

Fit map 5j2m.pdb map 3 in map cryosparc_P11_J21_004_volume_map_sharp.mrc using
100006 points  
correlation = 0.5642, correlation about mean = 0.06559, overlap = 3847  
steps = 56, shift = 0.263, angle = 0.78 degrees  
  
Position of 5j2m.pdb map 3 (#4) relative to
cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.90112104 -0.43300705 0.02204002 107.98669030  
-0.43216567 -0.90113064 -0.03458889 109.13954834  
0.03483817 0.02164384 -0.99915857 107.86114815  
Axis 0.97496166 -0.22189403 0.01458776  
Axis point 0.00000000 66.06940147 54.06555959  
Rotation angle (degrees) 178.34745060  
Shift along axis 82.63892115  
  
Average map value = 0.06837 for 9107 atoms, 6492 outside contour  

> ui tool show "Fit in Map"

Average map value = 0.06837 for 9107 atoms, 6492 outside contour  
Opened 5j2m.pdb map 2.5 as #4, grid size 96,130,158, pixel 0.833, shown at
level 0.13, step 1, values float32  

> fitmap #1 inMap #2 resolution 2.5

Fit map 5j2m.pdb map 2.5 in map cryosparc_P11_J21_004_volume_map_sharp.mrc
using 129371 points  
correlation = 0.5485, correlation about mean = 0.04106, overlap = 6702  
steps = 88, shift = 0.419, angle = 1.59 degrees  
  
Position of 5j2m.pdb map 2.5 (#4) relative to
cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.91140064 -0.41143390 0.00842775 108.37658117  
-0.41087370 -0.91092548 -0.03738410 109.27819215  
0.02305814 0.03060915 -0.99926543 107.92542679  
Axis 0.97759241 -0.21035259 0.00805433  
Axis point 0.00000000 65.34492294 54.64526088  
Rotation angle (degrees) 178.00708779  
Shift along axis 83.83043989  
  
Average map value = 0.06839 for 9107 atoms, 6468 outside contour  

> fitmap #1 inMap #2 resolution 2.5 metric correlation

Fit map 5j2m.pdb map 2.5 in map cryosparc_P11_J21_004_volume_map_sharp.mrc
using 129371 points  
correlation = 0.5491, correlation about mean = 0.04132, overlap = 6692  
steps = 68, shift = 0.622, angle = 1.49 degrees  
  
Position of 5j2m.pdb map 2.5 (#4) relative to
cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.90194890 -0.43128140 0.02201220 107.79126841  
-0.43044093 -0.90195612 -0.03457973 109.13593252  
0.03476763 0.02171420 -0.99915950 107.77168914  
Axis 0.97517395 -0.22096106 0.01455937  
Axis point 0.00000000 65.99124410 54.02394178  
Rotation angle (degrees) 178.34601149  
Shift along axis 82.56953292  
  
Average map value = 0.06835 for 9107 atoms, 6497 outside contour  

> fitmap #1 inMap #2 resolution 2.5

Fit map 5j2m.pdb map 2.5 in map cryosparc_P11_J21_004_volume_map_sharp.mrc
using 129371 points  
correlation = 0.5485, correlation about mean = 0.04107, overlap = 6702  
steps = 84, shift = 0.61, angle = 1.46 degrees  
  
Position of 5j2m.pdb map 2.5 (#4) relative to
cryosparc_P11_J21_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.91117467 -0.41193341 0.00846085 108.36504776  
-0.41137696 -0.91070722 -0.03716670 109.27506747  
0.02301556 0.03038475 -0.99927326 107.92186501  
Axis 0.97753469 -0.21062072 0.00805235  
Axis point 0.00000000 65.36378798 54.63648794  
Rotation angle (degrees) 178.01992522  
Shift along axis 83.78402463  
  
Average map value = 0.06839 for 9107 atoms, 6471 outside contour  
[Repeated 1 time(s)]Correlation = 0.5485, Correlation about mean = 0.04107,
Overlap = 6702  
  

> ui tool show "Fit to Segments"

Opened cryosparc_P11_J21_004_volume_map_sharp_masked as #5, grid size
256,256,256, pixel 0.84, shown at step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1856, in FitToEachRegion  
self.saFitMapToPoints ( fmap, tpoints, to_map )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1894, in saFitMapToPoints  
fpoints, fpoint_weights = fit_points(fmap)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 5187, in fit_points  
mat = fmap.data.full_matrix()  
AttributeError: 'NoneType' object has no attribute 'full_matrix'  
  
AttributeError: 'NoneType' object has no attribute 'full_matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 5187, in fit_points  
mat = fmap.data.full_matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 10 days, 12 hours, 15 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-OpenCommands: 1.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (3)

comment:1 by Eric Pettersen, 22 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Reporter: changed from chimerax-bug-report@… to rslack@…
Status: new → assigned
Summary: ChimeraX bug report submission → Segger: fmap.data is None

comment:2 by Tom Goddard, 22 months ago

You used Segger to fit an atomic model to a map. In order to do that it made a simulated map from the atomic model (it was model #4 in your Log output). Then you closed model #4 and tried to fit again. Unfortunately Segger doesn't realize you closed the simulated map, it remembers it and tries to use it again. To avoid this bug, don't close the simulated maps Segger produces if you are going to continue fitting the atomic model that the simulated map was created for.

comment:3 by Tom Goddard, 22 months ago

Resolution: → duplicate
Status: assigned → closed

Fixed in ChimeraX 1.7 daily builds and release candidate, July 25, 2023.

The segger code was fixed to check if the simulated map for an atomic model has been deleted and if so to recompute it.

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