Opened 4 years ago

Closed 4 years ago

#4804 closed defect (duplicate)

Map fit: 'NoneType' object has no attribute 'scene_position'

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version: 0.91
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/Dropbox/Post Doc/Gang
> Dong/3D-refinament/cryosparc_P230_J693_007_volume_map_sharp.mrc"

Opened cryosparc_P230_J693_007_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.06, shown at level 0.0201, step 1, values float32  

> volume #1 level 0.1272

> volume #1 level 0.08132

> volume #1 level 0.04307

> volume #1 level 0.06602

> close

> open "D:\Dropbox\Post Doc\Gang
> Dong\3D-refinament\cryosparc_P230_J693_007_volume_map_sharp.mrc"

Opened cryosparc_P230_J693_007_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.06, shown at level 0.0201, step 1, values float32  

> volume #1 level 0.2343

> open "D:/Dropbox/Post Doc/Gang
> Dong/3D-refinament/cryosparc_P230_J691_007_volume_map_sharp.mrc"

Opened cryosparc_P230_J691_007_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.06, shown at level 0.0223, step 1, values float32  

> volume #2 level 0.07096

> volume #2 level 0.064

> volume #2 level 0.2239

> volume #2 level 0.05705

> volume #2 level 0.05705

> volume #1 level 0.05837

> volume #2 level 0.1196

> volume #1 level 0.1043

> volume #1 level 0.09662

> volume #2 level 0.09877

> volume #2 level 0.1266

> volume #1 level 0.1272

> volume #2 level 0.1683

> volume #1 level 0.1578

> volume #2 level 0.09877

> volume #1 level 0.09662

> vop add #1.1 #1.2

> vop add #1 #2

> volume #3 level 0.1457

> toolshed show "Map Eraser"

> volume erase #3 center 130.78,105.88,124.24 radius 30.506 outside true

> save "D:/Dropbox/Post Doc/Gang Dong/3D-refinament/local/Subunit_1_dimer.mrc"
> models #3

Can only have one displayed volume when erasing  

Can only have one displayed volume when erasing  

Can only have one displayed volume when erasing  

Can only have one displayed volume when erasing  

> volume erase #1 center 140.38,166.77,126.14 radius 30.392 outside true

> save "D:/Dropbox/Post Doc/Gang Dong/3D-refinament/local/Subunit_2_dimer.mrc"
> models #2

> volume erase #1 center 135.44,133.23,173.26 radius 30.392 outside true

> save "D:/Dropbox/Post Doc/Gang
> Dong/3D-refinament/local/Subunit_v0_dimer.mrc" models #2

> open "D:/Dropbox/Post Doc/Gang
> Dong/3D-refinament/cryosparc_P230_J565_002_volume_map.mrc"

Opened cryosparc_P230_J565_002_volume_map.mrc, grid size 256,256,256, pixel
1.06, shown at level 0.0237, step 1, values float32  

> volume #2 level 0.05081

> volume #2 level 0.07145

> select #1

2 models selected  

> select #2

2 models selected  

> ~select #2

Nothing selected  

> select #2

2 models selected  

> ~select #2

Nothing selected  

> vop turn #1 y 180

Expected a density maps specifier or a keyword  

Expected an axis vector or a keyword  

> toolshed show "Fit in Map"

Correlation = 0.3447, Correlation about mean = -0.1613, Overlap = 423.7  
  
Fit map cryosparc_P230_J693_007_volume_map_sharp.mrc in map
cryosparc_P230_J565_002_volume_map.mrc using 33625 points  
correlation = 0.4893, correlation about mean = 0.03017, overlap = 650.2  
steps = 256, shift = 13.1, angle = 48.2 degrees  
  
Position of cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) relative to
cryosparc_P230_J565_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.73623778 -0.01963817 -0.67643793 121.10480710  
0.28393261 0.91630493 0.28243148 -68.74902906  
0.61427698 -0.39999951 0.68019422 15.27469714  
Axis -0.45762494 -0.86552829 0.20356866  
Axis point 60.89717867 0.00000000 160.15390075  
Rotation angle (degrees) 48.21260366  
Shift along axis 7.19309950  
  
Correlation = 0.4893, Correlation about mean = 0.03017, Overlap = 650.2  
  
Fit map cryosparc_P230_J693_007_volume_map_sharp.mrc in map
cryosparc_P230_J565_002_volume_map.mrc using 33625 points  
correlation = 0.4893, correlation about mean = 0.03012, overlap = 650.2  
steps = 80, shift = 0.00368, angle = 0.00653 degrees  
  
Position of cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) relative to
cryosparc_P230_J565_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.73618776 -0.01961885 -0.67649293 121.11965130  
0.28399327 0.91627097 0.28248068 -68.75777147  
0.61430889 -0.40007826 0.68011909 15.29298183  
Axis -0.45766709 -0.86550404 0.20357697  
Axis point 60.88705582 0.00000000 160.16126186  
Rotation angle (degrees) 48.21871677  
Shift along axis 7.19094933  
  
Correlation = 0.4893, Correlation about mean = 0.03012, Overlap = 650.2  
  
Fit map cryosparc_P230_J693_007_volume_map_sharp.mrc in map
cryosparc_P230_J565_002_volume_map.mrc using 33625 points  
correlation = 0.4892, correlation about mean = 0.02989, overlap = 650.2  
steps = 48, shift = 0.0198, angle = 0.0231 degrees  
  
Position of cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) relative to
cryosparc_P230_J565_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.73600430 -0.01970978 -0.67668988 121.19585953  
0.28395742 0.91638208 0.28215612 -68.71189472  
0.61454524 -0.39981923 0.68005788 15.22179248  
Axis -0.45723921 -0.86572532 0.20359760  
Axis point 60.98446604 0.00000000 160.15354603  
Rotation angle (degrees) 48.22384770  
Shift along axis 7.16924836  
  
Correlation = 0.2301, Correlation about mean = 0.131, Overlap = 382.2  
  
Fit map cryosparc_P230_J565_002_volume_map.mrc in map
cryosparc_P230_J693_007_volume_map_sharp.mrc using 55892 points  
correlation = 0.3033, correlation about mean = 0.1563, overlap = 461  
steps = 120, shift = 7.83, angle = 11.4 degrees  
  
Position of cryosparc_P230_J565_002_volume_map.mrc (#2) relative to
cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.70921842 0.16992353 0.68420408 -76.40188169  
-0.02574396 0.97611264 -0.21573449 38.09650595  
-0.70451862 0.13538876 0.69665156 112.81729992  
Axis 0.24286982 0.96057107 -0.13534202  
Axis point 94.81242753 0.00000000 152.94308412  
Rotation angle (degrees) 46.29136921  
Shift along axis 2.76976923  
  
Fit map cryosparc_P230_J565_002_volume_map.mrc in map
cryosparc_P230_J693_007_volume_map_sharp.mrc using 55892 points  
correlation = 0.3032, correlation about mean = 0.1562, overlap = 460.9  
steps = 76, shift = 0.0161, angle = 0.0169 degrees  
  
Position of cryosparc_P230_J565_002_volume_map.mrc (#2) relative to
cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.70922828 0.16970511 0.68424807 -76.38032447  
-0.02572213 0.97617667 -0.21544717 38.06312513  
-0.70450949 0.13520091 0.69669728 112.83092198  
Axis 0.24256034 0.96067116 -0.13518653  
Axis point 94.85422316 0.00000000 152.92267426  
Rotation angle (degrees) 46.28662872  
Shift along axis 2.78608836  
  
Fit map cryosparc_P230_J565_002_volume_map.mrc in map
cryosparc_P230_J693_007_volume_map_sharp.mrc using 55892 points  
correlation = 0.3032, correlation about mean = 0.1562, overlap = 461  
steps = 76, shift = 0.0104, angle = 0.0205 degrees  
  
Position of cryosparc_P230_J565_002_volume_map.mrc (#2) relative to
cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.70931436 0.16999566 0.68408670 -76.40187467  
-0.02587721 0.97610968 -0.21573192 38.12527156  
-0.70441714 0.13531950 0.69676763 112.79005718  
Axis 0.24285371 0.96055248 -0.13550281  
Axis point 94.80889273 0.00000000 152.95931915  
Rotation angle (degrees) 46.28308350  
Shift along axis 2.78347560  
  
Fit map cryosparc_P230_J693_007_volume_map_sharp.mrc in map
cryosparc_P230_J565_002_volume_map.mrc using 33625 points  
correlation = 0.4933, correlation about mean = 0.05478, overlap = 651.1  
steps = 148, shift = 8.09, angle = 12.3 degrees  
  
Position of cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) relative to
cryosparc_P230_J565_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.70548100 0.07331806 -0.70492626 114.93948848  
0.23277764 0.91548528 0.32817873 -67.55350661  
0.66941103 -0.39561493 0.62879066 13.57667703  
Axis -0.46354120 -0.88017068 0.10212315  
Axis point 60.12005508 0.00000000 142.90871565  
Rotation angle (degrees) 51.32673207  
Shift along axis 7.56592079  
  

> select #1

2 models selected  

> tile

> ~select #1

Nothing selected  

> select #1.1

1 model selected  

> ~select #1.1

Nothing selected  

> toolshed show "Map Coordinates"

Correlation = -0.005327, Correlation about mean = 0.00807, Overlap = -0.003044  
  
Fit map cryosparc_P230_J693_007_volume_map_sharp.mrc in map
cryosparc_P230_J565_002_volume_map.mrc using 33625 points  
correlation = 0.009511, correlation about mean = 0.001656, overlap = 0.004491  
steps = 2000, shift = 18, angle = 29.6 degrees  
  
Position of cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) relative to
cryosparc_P230_J565_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.79999962 -0.12361796 -0.58712794 44.19111943  
0.51301690 0.64838576 0.56250295 -108.74732541  
0.31114993 -0.75120870 0.58212646 129.69837432  
Axis -0.76642701 -0.52406053 0.37141648  
Axis point 0.00000000 49.57243720 157.89399738  
Rotation angle (degrees) 58.98543761  
Shift along axis 71.29302642  
  
Correlation = 0.009511, Correlation about mean = 0.001656, Overlap = 0.004491  
  
Correlation = 0.009511, Correlation about mean = 0.001656, Overlap = 0.004491  
  
Fit map cryosparc_P230_J693_007_volume_map_sharp.mrc in map
cryosparc_P230_J565_002_volume_map.mrc using 33625 points  
correlation = 0.01207, correlation about mean = 0.007765, overlap = 0.01933  
steps = 2000, shift = 43, angle = 61.2 degrees  
  
Position of cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) relative to
cryosparc_P230_J565_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.96062273 -0.10211836 -0.25841016 47.95198255  
0.04718297 0.97645951 -0.21047706 -133.06221069  
0.27382063 0.18999649 0.94282745 96.43194018  
Axis 0.58669047 -0.77971377 0.21872524  
Axis point -255.61593950 0.00000000 -122.79638071  
Rotation angle (degrees) 19.95602557  
Shift along axis 152.97550807  
  
Correlation = 0, Correlation about mean = 0, Overlap = 0  
  
Fit map cryosparc_P230_J693_007_volume_map_sharp.mrc in map
cryosparc_P230_J565_002_volume_map.mrc using 33625 points  
correlation = 0, correlation about mean = 0, overlap = 0  
steps = 24, shift = 0, angle = 0 degrees  
  
Position of cryosparc_P230_J693_007_volume_map_sharp.mrc (#1) relative to
cryosparc_P230_J565_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.96062273 -0.10211836 -0.25841016 47.95198255  
0.04718297 0.97645951 -0.21047706 -133.06221069  
0.27382063 0.18999649 0.94282745 96.43194018  
Axis 0.58669047 -0.77971377 0.21872524  
Axis point -255.61593950 0.00000000 -122.79638071  
Rotation angle (degrees) 19.95602557  
Shift along axis 152.97550807  
  

> open "D:/Dropbox/Post Doc/Gang
> Dong/3D-refinament/cryosparc_P230_J565_002_volume_map.mrc"

Opened cryosparc_P230_J565_002_volume_map.mrc, grid size 256,256,256, pixel
1.06, shown at level 0.0237, step 1, values float32  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\fit\fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.148201 Core Profile Forward-Compatible Context 20.50.02.10 27.20.15002.10002
OpenGL renderer: Radeon(TM) RX 550
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Map fit: 'NoneType' object has no attribute 'scene_position'
Version: → 0.91

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

Fixed 11 months ago, #3559.

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