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Opened 2 years ago
Closed 2 years ago
#10152 closed defect (fixed)
Sesson restore: wrapped C/C++ object of type DICOMTable has been deleted
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-166-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/media/roberto/DataDisk3/CirvSatellite/Images&Data/Cirv Capsid with
> C1and I3 comparison.cxs"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 139, in <lambda>
REMOVE_MODELS, lambda *args: self._remove_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 168, in _remove_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
Opened job041 postprocess_masked.mrc as #1, grid size 400,400,400, pixel 1.21,
shown at level 0.0108, step 1, values float32
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 136, in <lambda>
ADD_MODELS, lambda *args: self._add_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 175, in _add_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
Opened job062 postprocess_masked.mrc as #2, grid size 400,400,400, pixel 1.21,
shown at level 0.0058, step 1, values float32
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 136, in <lambda>
ADD_MODELS, lambda *args: self._add_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 175, in _add_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
Log from Tue Nov 14 16:35:09 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/media/roberto/DataDisk3/CirvSatellite/Images&Data/Cirv Capsid with
> C1and I3 comparison.cxs"
Opened job041 postprocess_masked.mrc as #1, grid size 400,400,400, pixel 1.21,
shown at level 0.0106, step 1, values float32
Opened job062 postprocess_masked.mrc as #2, grid size 400,400,400, pixel 1.21,
shown at level 0.00443, step 1, values float32
Log from Thu Jun 15 18:12:46 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/media/roberto/DataDisk3/CirvSatellite/Images&Data/Cirv Capsid with
> C1and I3 comparison.cxs" format session
Opened postprocess_masked.mrc as #1, grid size 400,400,400, pixel 1.21, shown
at level 0.0106, step 1, values float32
Opened postprocess_masked.mrc as #2, grid size 400,400,400, pixel 1.21, shown
at level 0.00443, step 1, values float32
Log from Thu Jun 15 18:09:34 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /media/roberto/DataDisk3/CirvSatellite/PostProcess/job041/postprocess_masked.mrc
Opened postprocess_masked.mrc as #1, grid size 400,400,400, pixel 1.21, shown
at level 0.0192, step 2, values float32
> open
> /media/roberto/DataDisk3/CirvSatellite/PostProcess/job062/postprocess_masked.mrc
Opened postprocess_masked.mrc as #2, grid size 400,400,400, pixel 1.21, shown
at level 0.016, step 2, values float32
> volume #1 level 0.01013
> volume #2 level 0.004429
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> fitmap #1 inMap #2 search 10
Found 1 unique fits from 10 random placements having fraction of points inside
contour >= 0.100 (1 of 10).
Correlations and times found:
-0.4006 (1)
Best fit found:
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 309341
points
correlation = -0.4006, correlation about mean = 0.2103, overlap = -36.4
steps = 384, shift = 61.9, angle = 9.28 degrees
Position of postprocess_masked.mrc (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.63026913 0.34738781 -0.69432162 173.32583714
-0.63933377 0.73961018 -0.21030710 270.18545974
0.44046922 0.57645335 0.68825026 -170.39244834
Axis 0.46357393 -0.66863993 -0.58139475
Axis point 410.89093549 0.00000000 31.66056421
Rotation angle (degrees) 58.05771196
Shift along axis -1.24217099
Found 1 fits.
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 309341
points
correlation = -0.4006, correlation about mean = 0.2103, overlap = -36.4
steps = 104, shift = 0.0228, angle = 0.00663 degrees
Position of postprocess_masked.mrc (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.63020367 0.34747004 -0.69433990 173.31038985
-0.63942061 0.73954736 -0.21026396 270.20782511
0.44043682 0.57648438 0.68824500 -170.37478262
Axis 0.46354405 -0.66859881 -0.58146586
Axis point 410.87104227 0.00000000 31.61885987
Rotation angle (degrees) 58.06221966
Shift along axis -1.25651065
> select add #1
2 models selected
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.76471,0.45754,-0.45374,56.218,-0.61399,0.73106,-0.2976,287.08,0.19555,0.50616,0.83998,-130.4
> fitmap #1 inMap #2
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 309341
points
correlation = -0.4166, correlation about mean = 0.2076, overlap = -37.82
steps = 56, shift = 2.09, angle = 0.652 degrees
Position of postprocess_masked.mrc (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.76990837 0.44887099 -0.45360326 56.36899158
-0.60560477 0.73803570 -0.29756700 282.54326485
0.20120621 0.50380364 0.84005832 -133.03401528
Axis 0.54239734 -0.44319931 -0.71370827
Axis point 426.38685071 93.34790402 0.00000000
Rotation angle (degrees) 47.62336427
Shift along axis 0.29888759
> fitmap #1 inMap #2
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 309341
points
correlation = -0.4166, correlation about mean = 0.2076, overlap = -37.82
steps = 116, shift = 0.00259, angle = 0.00282 degrees
Position of postprocess_masked.mrc (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.76991367 0.44886988 -0.45359537 56.36585919
-0.60560958 0.73801423 -0.29761046 282.56074442
0.20117147 0.50383608 0.84004718 -133.03328191
Axis 0.54243957 -0.44316299 -0.71369873
Axis point 426.40444059 93.36082590 0.00000000
Rotation angle (degrees) 47.62442348
Shift along axis 0.30029277
> fitmap #1 inMap #2
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 309341
points
correlation = -0.4166, correlation about mean = 0.2076, overlap = -37.82
steps = 84, shift = 0.0182, angle = 0.00295 degrees
Position of postprocess_masked.mrc (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.76993670 0.44884156 -0.45358429 56.35032090
-0.60557326 0.73804875 -0.29759876 282.53650224
0.20119263 0.50381075 0.84005730 -133.04526724
Axis 0.54243718 -0.44318833 -0.71368481
Axis point 426.39066975 93.37447144 0.00000000
Rotation angle (degrees) 47.62179901
Shift along axis 0.30201405
> view matrix models
> #1,0.75572,0.36433,-0.5442,102.11,-0.63017,0.63071,-0.45287,351.88,0.17824,0.68518,0.70623,-139.51
> view matrix models
> #1,0.75372,0.35091,-0.55567,108.61,-0.63342,0.61326,-0.47191,361.48,0.17518,0.70766,0.6845,-139.03
> fitmap #1 inMap #2
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 309341
points
correlation = -0.3904, correlation about mean = 0.2131, overlap = -35.43
steps = 168, shift = 1.14, angle = 9.4 degrees
Position of postprocess_masked.mrc (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.76489309 0.46790092 -0.44272709 50.49578614
-0.64116784 0.61916012 -0.45337017 357.32545449
0.06198665 0.63064210 0.77359435 -113.34297322
Axis 0.66466905 -0.30946846 -0.68003260
Axis point 478.55624755 132.62481288 0.00000000
Rotation angle (degrees) 54.63214376
Shift along axis 0.05894491
> view matrix models
> #1,0.75541,0.48716,-0.43821,47.018,-0.64825,0.65308,-0.39147,335.93,0.095477,0.57979,0.80915,-117.61
> fitmap #1 inMap #2
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 309341
points
correlation = -0.3881, correlation about mean = 0.2114, overlap = -35.25
steps = 176, shift = 2.83, angle = 3.85 degrees
Position of postprocess_masked.mrc (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.78866217 0.45594622 -0.41246213 41.20956462
-0.61135602 0.65273996 -0.44740845 339.02695663
0.06523634 0.60501534 0.79353682 -114.79493262
Axis 0.66897451 -0.30364964 -0.67843202
Axis point 478.94615186 135.28900970 0.00000000
Rotation angle (degrees) 51.86842290
Shift along axis 2.50329383
> view matrix models
> #1,0.72369,0.68443,0.088479,-118.9,-0.64023,0.71369,-0.28418,292.01,-0.25765,0.14901,0.95468,35.675
> fitmap #1 inMap #2
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 309341
points
correlation = -0.4012, correlation about mean = 0.2097, overlap = -36.43
steps = 84, shift = 1.91, angle = 2.81 degrees
Position of postprocess_masked.mrc (#1) relative to postprocess_masked.mrc
(#2) coordinates:
Matrix rotation and translation
0.71614410 0.68894236 0.11178569 -124.93318517
-0.62905266 0.70650345 -0.32426160 302.00250255
-0.30237453 0.16189897 0.93933933 47.96708195
Axis 0.33194561 0.28278448 -0.89991391
Axis point 331.28355426 318.20324903 0.00000000
Rotation angle (degrees) 47.07867662
Shift along axis 0.76435398
> select subtract #1
Nothing selected
> ui tool show "Side View"
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.01058
> surface dust #1 size 12.1
> volume #1 color #f79b9b
> volume #1 color #f37e7e
> vop subtract #1 #2 minrms True
Opened volume difference as #3, grid size 400,400,400, pixel 1.21, shown at
step 1, values float32
Minimum RMS scale factor for "postprocess_masked.mrc #2" above level 0.004429
is 0.27798
> volume #3 level 0.0193
> volume #3 level 0.02534
> volume #3 level 0.0287
> volume #3 level 0.02685
> volume #3 level 0.02383
> surface dust #3 size 12.1
> volume #3 level 0.02266
> close #3
> show #!2 models
> show #!1 models
> surface dust #1 size 12.1
> surface dust #2 size 12.1
> save "/media/roberto/DataDisk3/CirvSatellite/Images&Data/Cirv Capsid with
> C1and I3 comparison.cxs" includeMaps true
——— End of log from Thu Jun 15 18:09:34 2023 ———
opened ChimeraX session
> rename #1 "job041 postprocess_masked.mrc"
> rename #2 "job062 postprocess_masked.mrc"
> save "/media/roberto/DataDisk3/CirvSatellite/Images&Data/Cirv Capsid with
> C1and I3 comparison.cxs" includeMaps true
——— End of log from Thu Jun 15 18:12:46 2023 ———
opened ChimeraX session
> vop subtract #1 #2 minrms True
Opened volume difference as #3, grid size 400,400,400, pixel 1.21, shown at
step 1, values float32
Minimum RMS scale factor for "job062 postprocess_masked.mrc #2" above level
0.004429 is 0.27798
> volume #3 level 0.01628
> volume #3 level 0.03188
> close #3
> show #!2 models
> show #!1 models
> volume #2 level 0.005803
> lighting shadows true
> volume #1 level 0.009353
> volume #1 level 0.009506
> volume #1 level 0.01134
> volume #1 level 0.01042
> map filter #1 Gaussian
Unknown command: map filter #1 Gaussian
> toolshed show
> ui tool show "Volume Viewer"
> ui tool show "DICOM Browser"
> volume gaussian #1 sDev 5
Opened job041 postprocess_masked.mrc gaussian as #3, grid size 400,400,400,
pixel 1.21, shown at step 1, values float32
> volume #3 level 0.005633
> close #3
> show #!1 models
> volume gaussian #1 sDev 3
Opened job041 postprocess_masked.mrc gaussian as #3, grid size 400,400,400,
pixel 1.21, shown at step 1, values float32
> volume #3 level 0.005815
> close #3
> show #!1 models
> volume subtract #2 #1 modelld #3
Expected a keyword
> volume subtract #2 #1 modelId #3
Opened volume difference as #3, grid size 400,400,400, pixel 1.21, shown at
step 1, values float32
> volume subtract #1 #2 modelId #4
Opened volume difference as #4, grid size 400,400,400, pixel 1.21, shown at
step 1, values float32
> hide #!3 models
> close #4
> show #!3 models
> volume #3 level -0.005071
> volume #3 level -0.0203
> volume #3 level 0.01357
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #3
> volume subtract #1 #2 modelId #4
Opened volume difference as #4, grid size 400,400,400, pixel 1.21, shown at
step 1, values float32
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #1 level -0.008522
> volume #1 level 0.01989
> close #4
> show #!2 models
> hide #!1 models
> show #!1 models
> select add #2
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models #2,1,0,0,1.0999,0,1,0,-2.2513,0,0,1,-0.97632
> select subtract #2
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.71614,0.68894,0.11179,-124.86,-0.62905,0.7065,-0.32426,302.53,-0.30237,0.1619,0.93934,49.489
> view matrix models
> #1,0.73836,0.60797,0.2919,-154.19,-0.57236,0.79382,-0.20557,238.58,-0.35669,-0.015288,0.9341,107.29
> view matrix models
> #1,-0.0837,-0.98087,0.17576,462.61,-0.94913,0.024742,-0.31391,544.63,0.30356,-0.19309,-0.93304,442.66
> view matrix models
> #1,-0.0837,-0.98087,0.17576,194.39,-0.94913,0.024742,-0.31391,434.12,0.30356,-0.19309,-0.93304,711.67
> volume #1 level 0.01551
> volume #1 level 0.0131
> volume #1 level 0.01084
> view matrix models
> #1,0.18411,-0.3528,0.91741,-202.07,-0.35465,-0.89433,-0.27275,503.68,0.91669,-0.27514,-0.28978,427.98
> lighting soft
> view matrix models
> #1,0.31633,-0.34995,0.88174,-226.19,-0.28969,-0.92071,-0.26149,491.65,0.90334,-0.17272,-0.39262,431.1
> view matrix models
> #1,0.41907,-0.16811,0.89226,-297.84,-0.034406,-0.98494,-0.16942,423.22,0.9073,0.040298,-0.41854,384.59
> view matrix models
> #1,0.41691,-0.16288,0.89423,-209.24,-0.026381,-0.98557,-0.16722,446.11,0.90856,0.046124,-0.41519,303.37
> transparency sel 50
> transparency sel 0
> transparency 40
> transparency 0
> volume #1 transparency 40
> volume #1 transparency 20
> volume #1 transparency 0
> volume #1 transparency 1
> transparency #1 40
> transparency #1 20
> lighting soft
> view matrix models
> #1,-0.48167,-0.41592,0.77137,99.621,0.0021429,-0.88076,-0.47356,487.58,0.87635,-0.22645,0.42513,174.84
> view matrix models
> #1,-0.48167,-0.41592,0.77137,66.291,0.0021429,-0.88076,-0.47356,412.03,0.87635,-0.22645,0.42513,334.69
> transparency #1 0
> view matrix models
> #1,-0.3918,-0.0037973,0.92004,-91.555,-0.14198,-0.98776,-0.064538,374.34,0.90903,-0.15591,0.38646,318.94
> view matrix models
> #1,-0.33989,0.091935,0.93596,-131.25,-0.16629,-0.9854,0.036404,355.32,0.92565,-0.14327,0.35022,320.58
> view matrix models
> #1,-0.33989,0.091935,0.93596,-129.83,-0.16629,-0.9854,0.036404,345.85,0.92565,-0.14327,0.35022,308.02
> view matrix models
> #1,-0.19092,0.054547,0.98009,-167.47,-0.16993,-0.98522,0.021729,350.23,0.96678,-0.1624,0.19737,339.56
> view matrix models
> #1,-0.3739,-0.041127,0.92656,-86.966,-0.14339,-0.98444,-0.10156,373.34,0.91632,-0.17083,0.36218,314.09
> view matrix models
> #1,-0.28797,-0.40984,0.86551,-3.3929,-0.095224,-0.88706,-0.45173,422.42,0.95289,-0.2125,0.21642,350.52
> view matrix models
> #1,-0.36364,-0.0061579,0.93152,-99.151,-0.20981,-0.97374,-0.088341,383.64,0.9076,-0.22756,0.3528,332.26
> view matrix models
> #1,-0.36364,-0.0061579,0.93152,-105.45,-0.20981,-0.97374,-0.088341,393.03,0.9076,-0.22756,0.3528,373.22
> view matrix models
> #1,-0.36364,-0.0061579,0.93152,64.975,-0.20981,-0.97374,-0.088341,573.12,0.9076,-0.22756,0.3528,-22.643
> view matrix models
> #1,-0.36364,-0.0061579,0.93152,108.5,-0.20981,-0.97374,-0.088341,546.27,0.9076,-0.22756,0.3528,-3.2764
> view matrix models
> #1,-0.65943,-0.34534,0.66776,326.24,0.042454,-0.90394,-0.42555,549.49,0.75057,-0.25227,0.61074,-21.418
> view matrix models
> #1,-0.65455,-0.34228,0.6741,322.79,0.037764,-0.90534,-0.42302,550.35,0.75508,-0.25143,0.60551,-21.455
> view matrix models
> #1,-0.63593,-0.34033,0.69265,313.33,0.025721,-0.90636,-0.42171,553.21,0.77131,-0.25037,0.58514,-20.735
> view matrix models
> #1,-0.67048,-0.11883,0.73235,258.26,-0.046318,-0.97846,-0.20117,535.01,0.74048,-0.1688,0.65053,-48.868
> view matrix models
> #1,-0.34593,-0.18582,0.91968,150.76,-0.19835,-0.94355,-0.26526,578.81,0.91706,-0.27418,0.28954,21.025
> view matrix models
> #1,-0.77854,-0.11868,0.61627,312.39,0.023535,-0.98679,-0.16031,510.26,0.62715,-0.1103,0.77105,-64.698
> view matrix models
> #1,-0.62819,-0.43246,0.6468,344.92,0.099085,-0.869,-0.48479,541.55,0.77172,-0.24045,0.58875,-24.114
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map job062 postprocess_masked.mrc in map job041 postprocess_masked.mrc
using 1374311 points
correlation = 0.4658, correlation about mean = 0.03811, overlap = 120
steps = 140, shift = 5.47, angle = 6.12 degrees
Position of job062 postprocess_masked.mrc (#2) relative to job041
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.59571020 0.18850096 0.78076682 152.24224661
-0.45928134 -0.87741322 -0.13858858 600.08376453
0.65893103 -0.44115020 0.60925895 40.09923960
Axis -0.41717386 0.16798796 -0.89316629
Axis point 129.78607163 287.75062404 0.00000000
Rotation angle (degrees) 158.73804357
Shift along axis 1.48007356
> volume #1 rotate 20
Expected a keyword
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.75599,-0.23628,0.61045,336.93,-0.28143,-0.72466,-0.62902,633.42,0.591,-0.64733,0.48134,144.52
> view matrix models
> #1,-0.75599,-0.23628,0.61045,337.88,-0.28143,-0.72466,-0.62902,641.96,0.591,-0.64733,0.48134,154.78
> view matrix models
> #1,-0.78122,-0.14248,0.60778,321.82,-0.41206,-0.61368,-0.6735,657.35,0.46895,-0.77659,0.42071,230.4
> view matrix models
> #1,-0.79631,-0.10321,0.59602,318.76,-0.40981,-0.6327,-0.65708,657.47,0.44492,-0.76749,0.46153,224.16
> view matrix models
> #1,-0.80047,-0.069708,0.5953,310.93,-0.41664,-0.64929,-0.63627,657.38,0.43087,-0.75734,0.49069,219.68
> fitmap #2 inMap #1
Fit map job062 postprocess_masked.mrc in map job041 postprocess_masked.mrc
using 1374311 points
correlation = 0.8936, correlation about mean = 0.411, overlap = 380.2
steps = 116, shift = 14.3, angle = 5.9 degrees
Position of job062 postprocess_masked.mrc (#2) relative to job041
postprocess_masked.mrc (#1) coordinates:
Matrix rotation and translation
-0.79742650 -0.30629798 0.51989673 383.80065721
-0.09809175 -0.78432749 -0.61254264 604.81589455
0.59538984 -0.53945526 0.59539821 84.04694210
Axis 0.31338605 -0.32370138 0.89275226
Axis point 157.33614691 330.22565356 0.00000000
Rotation angle (degrees) 173.30355085
Shift along axis -0.46886777
> select add #1
4 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save "/media/roberto/DataDisk3/CirvSatellite/Images&Data/Cirv Capsid with
> C1and I3 comparison.cxs" includeMaps true
——— End of log from Tue Nov 14 16:35:09 2023 ———
opened ChimeraX session
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 139, in <lambda>
REMOVE_MODELS, lambda *args: self._remove_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 168, in _remove_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 139, in <lambda>
REMOVE_MODELS, lambda *args: self._remove_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 168, in _remove_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
> hide #!1 models
> open /media/roberto/DataDisk3/CirvSatellite/Images&Data/HomologyModel_01.pdb
HomologyModel_01.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) capsid protein [more
info...]
Chain information for HomologyModel_01.pdb #3
---
Chain | Description
A B | No description available
C | No description available
Non-standard residues in HomologyModel_01.pdb #3
---
CA — (CA)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 136, in <lambda>
ADD_MODELS, lambda *args: self._add_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 175, in _add_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
> select add #3
6766 atoms, 6889 bonds, 903 residues, 1 model selected
> view matrix models
> #3,0.96022,0.26997,0.071346,-17.86,-0.27637,0.95535,0.10457,-14.172,-0.039928,-0.12013,0.99195,4.459
> view matrix models
> #3,0.96022,0.26997,0.071346,424.23,-0.27637,0.95535,0.10457,320.17,-0.039928,-0.12013,0.99195,-109.27
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 136, in <lambda>
ADD_MODELS, lambda *args: self._add_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 175, in _add_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
> view matrix models
> #3,0.96022,0.26997,0.071346,463.53,-0.27637,0.95535,0.10457,227.09,-0.039928,-0.12013,0.99195,-49.676
> view matrix models
> #3,0.90128,0.28095,-0.32979,518,-0.2781,0.95887,0.056865,233.53,0.3322,0.040464,0.94234,-46.049
> view matrix models
> #3,0.90128,0.28095,-0.32979,519.56,-0.2781,0.95887,0.056865,178.59,0.3322,0.040464,0.94234,-40.672
> view matrix models
> #3,0.5002,0.24794,-0.82966,587.47,-0.22226,0.96279,0.15373,165.41,0.8369,0.1075,0.53669,15.09
> view matrix models
> #3,0.5002,0.24794,-0.82966,740.84,-0.22226,0.96279,0.15373,112.21,0.8369,0.1075,0.53669,232.08
> view matrix models
> #3,0.33287,0.51728,-0.78842,726.61,-0.70035,0.69549,0.16062,117.14,0.63143,0.49871,0.59379,211.94
> view matrix models
> #3,0.11544,0.64067,-0.75909,718.08,-0.93268,0.33283,0.13907,129.77,0.34174,0.69193,0.63596,199.31
> view matrix models
> #3,-0.15156,0.65824,-0.73739,713.5,-0.98807,-0.12156,0.094575,148.95,-0.027385,0.74293,0.66881,191.8
> view matrix models
> #3,-0.4963,0.46621,-0.73235,717.02,-0.69106,-0.72275,0.0082228,179.63,-0.52547,0.51018,0.68088,194.92
> view matrix models
> #3,-0.4963,0.46621,-0.73235,719.5,-0.69106,-0.72275,0.0082228,182.78,-0.52547,0.51018,0.68088,198.2
> view matrix models
> #3,-0.4963,0.46621,-0.73235,712.35,-0.69106,-0.72275,0.0082228,175.26,-0.52547,0.51018,0.68088,188.67
> view matrix models
> #3,-0.56805,0.36444,-0.73791,715.81,-0.52316,-0.85204,-0.01807,183.34,-0.63531,0.37578,0.67466,193.01
> view matrix models
> #3,-0.56805,0.36444,-0.73791,711.25,-0.52316,-0.85204,-0.01807,199.57,-0.63531,0.37578,0.67466,185.72
> view matrix models
> #3,-0.62853,0.20385,-0.7506,717.45,-0.25325,-0.96609,-0.050302,208.44,-0.7354,0.15847,0.65884,193.84
> view matrix models
> #3,-0.081359,0.66566,-0.74181,704.96,-0.99416,-0.0012724,0.10789,155.44,0.070877,0.74626,0.66188,179.51
> view matrix models
> #3,-0.55452,0.3875,-0.73644,710.43,-0.56147,-0.8274,-0.012591,197.94,-0.61421,0.40651,0.67638,184.67
> view matrix models
> #3,-0.72665,-0.19824,0.65779,535.58,-0.44669,0.86378,-0.23314,179.14,-0.52197,-0.46324,-0.71621,401.6
> view matrix models
> #3,-0.87923,-0.18542,0.43883,564.62,-0.3709,0.84453,-0.38627,201.02,-0.29898,-0.50239,-0.81131,416.71
> view matrix models
> #3,-0.8336,-0.27441,0.47939,561.85,-0.50329,0.73496,-0.45445,213.05,-0.22762,-0.6201,-0.75077,412.14
> view matrix models
> #3,-0.94497,-0.1825,0.27152,587.22,-0.32066,0.68121,-0.65812,243.31,-0.064858,-0.70898,-0.70224,408.75
> view matrix models
> #3,-0.99025,0.1318,-0.045099,621.28,0.097726,0.42656,-0.89917,285.56,-0.099275,-0.89481,-0.43528,377.42
> view matrix models
> #3,-0.94489,0.037945,0.32518,573.4,-0.32719,-0.075338,-0.94195,304.39,-0.011244,-0.99644,0.083602,309.56
> view matrix models
> #3,-0.71553,0.1768,0.67584,522.16,-0.61807,-0.6111,-0.4945,257.5,0.32558,-0.77155,0.54654,240.83
> view matrix models
> #3,-0.97658,0.045547,0.2103,588.81,-0.20589,0.086093,-0.97478,304.66,-0.062504,-0.99525,-0.074698,331.04
> view matrix models
> #3,-0.8617,0.067955,0.50284,548.49,-0.49432,-0.33607,-0.80169,292.1,0.11451,-0.93938,0.32319,275.53
> view matrix models
> #3,-0.64256,0.24584,0.72573,513.59,-0.63532,-0.70041,-0.32525,236.82,0.42835,-0.67007,0.60624,230.09
> view matrix models
> #3,-0.97228,0.042914,0.22985,586.23,-0.22719,0.058975,-0.97206,305,-0.05527,-0.99734,-0.04759,327.41
> view matrix models
> #3,-0.78673,0.118,0.60591,533.19,-0.5753,-0.496,-0.65039,275.69,0.22379,-0.86027,0.45811,255.15
> view matrix models
> #3,-0.25112,0.79272,0.55545,522.54,-0.19325,-0.60335,0.77371,84.996,0.94847,0.08695,0.30471,251.42
> view matrix models
> #3,-0.63939,0.24902,0.72744,513.28,-0.63552,-0.70369,-0.3177,235.88,0.43278,-0.66543,0.60819,229.71
> view matrix models
> #3,-0.30258,0.68775,0.65988,511.08,-0.35153,-0.72405,0.59345,112.62,0.88593,-0.052402,0.46085,233.82
> view matrix models
> #3,0.1031,0.36023,0.92715,485.66,-0.11222,-0.92195,0.37069,149.96,0.98832,-0.14226,-0.054633,307.6
> view matrix models
> #3,0.86985,-0.11263,0.48028,563.96,-0.13056,-0.99143,0.0039733,202.24,0.47572,-0.066163,-0.87711,416.13
> view matrix models
> #3,0.77498,-0.31928,-0.54541,710.36,-0.50705,-0.82925,-0.23504,228.74,-0.37724,0.4587,-0.80454,387.31
> view matrix models
> #3,0.86504,-0.49435,0.085596,629.28,-0.46346,-0.85272,-0.24097,230.42,0.19211,0.16878,-0.96675,420.39
> view matrix models
> #3,0.973,0.021082,0.22986,594.83,-0.031375,-0.9745,0.22219,172.2,0.22868,-0.2234,-0.94752,429.38
> view matrix models
> #3,0.22551,-0.50732,0.83172,524.66,-0.13121,-0.86175,-0.49006,266.22,0.96536,0.0013869,-0.2609,331.6
> view matrix models
> #3,0.10366,-0.21856,0.9703,496.69,-0.27604,-0.94355,-0.18305,225.9,0.95554,-0.24887,-0.15814,324.79
> view matrix models
> #3,0.075418,0.14565,0.98646,483.69,-0.45895,-0.87319,0.16402,175.47,0.88526,-0.4651,0.00099358,309.01
> view matrix models
> #3,-0.33124,0.25203,0.90927,489.5,-0.38848,-0.91463,0.11199,184.11,0.85986,-0.31613,0.40087,249.67
> select subtract #3
Nothing selected
> select add #3
6766 atoms, 6889 bonds, 903 residues, 1 model selected
> hide #!2 models
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 139, in <lambda>
REMOVE_MODELS, lambda *args: self._remove_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 168, in _remove_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
> view matrix models
> #3,0.60944,-0.42747,0.66772,546.4,-0.32334,-0.90298,-0.28296,238.23,0.7239,-0.043453,-0.68853,390.61
> view matrix models
> #3,0.64352,-0.25217,0.7227,533.86,-0.30008,-0.95171,-0.064868,209.82,0.70415,-0.17513,-0.68811,394.32
> view matrix models
> #3,0.49241,-0.4814,0.72511,539.62,-0.70035,-0.71379,0.0017129,192.08,0.51676,-0.50868,-0.68863,403.4
> show #!2 models
> view matrix models
> #3,0.48047,-0.3917,0.78468,528.77,-0.65487,-0.75536,0.023919,190.44,0.58335,-0.52536,-0.61944,394.66
> view matrix models
> #3,0.17802,-0.53,0.8291,525.49,-0.58419,-0.73494,-0.34438,240.66,0.79186,-0.42304,-0.44045,367.96
> view matrix models
> #3,0.24533,-0.51598,0.82072,526.51,-0.59521,-0.7484,-0.2926,233.91,0.7652,-0.41672,-0.49072,374.57
> view matrix models
> #3,0.24533,-0.51598,0.82072,402.7,-0.59521,-0.7484,-0.2926,279.47,0.7652,-0.41672,-0.49072,199.25
> view matrix models
> #3,-0.49587,0.47495,-0.727,583.01,0.75564,-0.17656,-0.63075,314.65,-0.42793,-0.86212,-0.27134,177.31
> view matrix models
> #3,0.0022419,0.62956,-0.77695,587.37,0.86607,-0.38963,-0.31322,277.77,-0.49992,-0.67219,-0.54611,209.16
> view matrix models
> #3,0.0022419,0.62956,-0.77695,393.75,0.86607,-0.38963,-0.31322,224.21,-0.49992,-0.67219,-0.54611,246.26
> view matrix models
> #3,-0.32139,0.77991,0.53708,207.73,0.86331,0.47437,-0.17223,179.55,-0.3891,0.40831,-0.82576,253.44
> view matrix models
> #3,-0.32139,0.77991,0.53708,246.38,0.86331,0.47437,-0.17223,240.18,-0.3891,0.40831,-0.82576,293.43
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule HomologyModel_01.pdb (#3) to map job062 postprocess_masked.mrc
(#2) using 6766 atoms
average map value = 5.395e-05, steps = 180
shifted from previous position = 29.1
rotated from previous position = 20 degrees
atoms outside contour = 4988, contour level = 0.0058031
Position of HomologyModel_01.pdb (#3) relative to job062
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.14121513 0.68180054 0.71777857 242.39475895
0.64615658 0.61278535 -0.45494567 241.91881925
-0.75002647 0.39955216 -0.52708456 225.85629378
Axis 0.50300370 0.86402953 -0.02098196
Axis point 125.64737942 0.00000000 90.67079717
Rotation angle (degrees) 121.85404424
Shift along axis 326.21155703
> view matrix models
> #3,-0.039114,0.58269,0.81175,236.91,0.76957,0.53574,-0.34749,250.26,-0.63736,0.61111,-0.46938,223.78
> view matrix models
> #3,-0.039114,0.58269,0.81175,241.67,0.76957,0.53574,-0.34749,255.31,-0.63736,0.61111,-0.46938,229.31
> view matrix models
> #3,-0.16435,0.57925,0.79841,243.09,0.80925,0.54199,-0.22664,238.7,-0.56401,0.60886,-0.55784,241.81
> view matrix models
> #3,-0.13492,0.58212,0.80183,242.66,0.80132,0.54009,-0.25727,242.93,-0.58283,0.60781,-0.53933,239.23
> view matrix models
> #3,-0.10739,0.66715,0.73714,249.16,0.794,0.50377,-0.34026,255.35,-0.59835,0.54875,-0.58382,247
> view matrix models
> #3,-0.10739,0.66715,0.73714,243.53,0.794,0.50377,-0.34026,251.51,-0.59835,0.54875,-0.58382,239.94
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 139, in <lambda>
REMOVE_MODELS, lambda *args: self._remove_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 168, in _remove_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
Opened HomologyModel_01.pdb map 4 as #4, grid size 95,89,74, pixel 1.33, shown
at level 0.098, step 1, values float32
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 136, in <lambda>
ADD_MODELS, lambda *args: self._add_patient(*args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 175, in _add_patient
self._resync_tables()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/dicom/ui/dicom_browser.py", line 178, in _resync_tables
self.patient_table.data = []
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 473, in data
emit_signal = self.selected
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type DICOMTable has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_table.py", line 567, in selected
for i in self.selectionModel().selectedRows()]
See log for complete Python traceback.
> fitmap #3 inMap #2 resolution 4
Fit map HomologyModel_01.pdb map 4 in map job062 postprocess_masked.mrc using
43224 points
correlation = -0.01521, correlation about mean = 0.02711, overlap = -3.436
steps = 76, shift = 1.96, angle = 1.87 degrees
Position of HomologyModel_01.pdb map 4 (#4) relative to job062
postprocess_masked.mrc (#2) coordinates:
Matrix rotation and translation
-0.13221136 0.68259691 0.71873595 242.36306145
0.64480109 0.60993841 -0.46065873 243.00619172
-0.75282896 0.40253743 -0.52078011 224.69167494
Axis 0.50583733 0.86234450 -0.02214854
Axis point 125.32351885 0.00000000 90.47391186
Rotation angle (degrees) 121.43470779
Shift along axis 327.17474390
Average map value = 5.763e-06 for 6766 atoms, 5014 outside contour
OpenGL version: 3.3.0 NVIDIA 525.147.05
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=unity
XDG_SESSION_DESKTOP=unity
XDG_CURRENT_DESKTOP=Unity:Unity7:ubuntu
DISPLAY=:0
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 28 Intel(R) Core(TM) i9-7940X CPU @ 3.10GHz
Cache Size: 19712 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 5.5Gi 97Gi 92Mi 22Gi 118Gi
Swap: 18Gi 0B 18Gi
Graphics:
1a:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti Rev. A] [10de:1e07] (rev a1)
Subsystem: ASUSTeK Computer Inc. TU102 [GeForce RTX 2080 Ti Rev. A] [1043:866a]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
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: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Sesson restore: wrapped C/C++ object of type DICOMTable has been deleted |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Should be fixed in tomorrow's daily build and the 1.7 release.