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Opened 4 years ago
Closed 4 years ago
#4766 closed defect (fixed)
Structure positions is None (Segger holding ref to dead Structure)
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | gregdp@… | |
| 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: 1.1 (2020-09-09 22:22:27 UTC)
Description
While saving CHimeraX session on Windows I got this error and session could not be saved
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/Nox5_data/EGTA state/j71_flip.mrc"
Opened j71_flip.mrc, grid size 320,320,320, pixel 0.826, shown at level 0.248,
step 2, values float32
> volume #1 level 0.3717
> volume #1 step 1
> set bgColor white
> ui tool show "Segment Map"
Segmenting j71_flip.mrc, density threshold 0.371672
Showing j71_flip.seg - 0 regions, 0 surfaces
Only showing 10 of 105 regions.
Showing 10 of 105 region surfaces
1699 watershed regions, grouped to 105 regions
Segmenting j71_flip.mrc, density threshold 0.371672
Showing j71_flip.seg - 0 regions, 0 surfaces
Only showing 10 of 105 regions.
Showing 10 of 105 region surfaces
1699 watershed regions, grouped to 105 regions
> volume #1 level 0.4418
> surface style #2.1-10 mesh
> surface hidePatches #2.1-10
> transparency #2.1-10 30
> open "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/Nox5_data/New/EGTA/two_heme/round2/Sun/EGTA-f_real_space_refined-
> coot-2_sequence corrected.pdb"
Summary of feedback from opening C:/Users/njain04/OneDrive - St. Jude
Children's Research Hospital/Nox5_data/New/EGTA/two_heme/round2/Sun/EGTA-
f_real_space_refined-coot-2_sequence corrected.pdb
---
warning | Ignored bad PDB record found on line 10314
END
Chain information for EGTA-f_real_space_refined-coot-2_sequence corrected.pdb
#3
---
Chain | Description
A C | No description available
> volume #1 level 0.4099
> volume #1 level 0.3589
> surface hidePatches #2.1-10
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
QWindowsWindow::setGeometry: Unable to set geometry 1920x1068-1920+27 (frame:
1938x1113-1929-9) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY3". Resulting geometry: 1920x1005-1920+27 (frame:
1938x1050-1929-9) margins: 9, 36, 9, 9 minimum size: 700x1068 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=718,1113 maxtrack=0,0)
Simulating map res 4.000, grid 2.000
> molmap #3 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false
Top score: 0.46880, z-score: 2.80698 (avg: 0.4419, stdev: 0.0096)
Top score: 0.46880, z-score: 2.80698 (avg: 0.4419, stdev: 0.0096)
QWindowsWindow::setGeometry: Unable to set geometry 1920x1565-1920+27 (frame:
1938x1610-1929-9) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY3". Resulting geometry: 1920x1005-1920+27 (frame:
1938x1050-1929-9) margins: 9, 36, 9, 9 minimum size: 700x1565 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=718,1610 maxtrack=0,0)
> hide #!2 models
> show #!1 models
> close #2
> volume #4 level 0.131
> close #4
> ui tool show "Fit in Map"
> select #3
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 3 models selected
> ~select #3
Nothing selected
> close #3
> open "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/Nox5_data/New/EGTA/two_heme/round2/Sun/EGTA-f_real_space_refined-
> coot-2_sequence corrected.pdb"
Summary of feedback from opening C:/Users/njain04/OneDrive - St. Jude
Children's Research Hospital/Nox5_data/New/EGTA/two_heme/round2/Sun/EGTA-
f_real_space_refined-coot-2_sequence corrected.pdb
---
warning | Ignored bad PDB record found on line 10314
END
Chain information for EGTA-f_real_space_refined-coot-2_sequence corrected.pdb
#2
---
Chain | Description
A C | No description available
Segmenting j71_flip.mrc, density threshold 0.358920
Showing j71_flip.seg - 0 regions, 0 surfaces
Only showing 60 of 109 regions.
Showing 60 of 109 region surfaces
1846 watershed regions, grouped to 109 regions
> hide #!1 models
> transparency #2-3 40
Grouped 4 regions
Grouped 1 regions
Grouped 2 regions
Grouped 2 regions
Grouped 1 regions
Grouped 1 regions
Grouped 3 regions
Grouped 3 regions
Grouped 2 regions
Drag select of 2641, 13 of 19284 triangles, 2631, 88 of 19264 triangles, 2561,
60 of 13976 triangles, 2659, 87 of 10032 triangles, 3 residues
> transparency #3.28 40
> select
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 56 models selected
> transparency (#!2 & sel) 40
> hide #1.1 models
> show #1.1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> transparency (#!2 & sel) 40
> select #1
2 models selected
> transparency #1.1 40
> ui tool show "Show Volume Menu"
> surface hidePatches #1.1
> select #2
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 3 models selected
> select #3
51 models selected
> select #2
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 3 models selected
> close #3
Fit molecule EGTA-f_real_space_refined-coot-2_sequence corrected.pdb (#2) to
map j71_flip.mrc (#1) using 10190 atoms
average map value = 0.6754, steps = 44
shifted from previous position = 0.00436
rotated from previous position = 0.0203 degrees
atoms outside contour = 2135, contour level = 0.35892
Position of EGTA-f_real_space_refined-coot-2_sequence corrected.pdb (#2)
relative to j71_flip.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00003678 -0.00010872 0.01873159
0.00003681 0.99999994 0.00033525 -0.05293917
0.00010870 -0.00033526 0.99999994 0.03277577
Axis -0.94609898 -0.30678224 0.10383347
Axis point 0.00000000 97.13848809 156.16508059
Rotation angle (degrees) 0.02030314
Shift along axis 0.00192208
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
QWindowsWindow::setGeometry: Unable to set geometry 1920x998-1920+27 (frame:
1938x1043-1929-9) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY3". Resulting geometry: 1920x956-1920+27 (frame:
1938x1001-1929-9) margins: 9, 36, 9, 9 minimum size: 582x998 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=600,1043 maxtrack=0,0)
> ui tool show "Color Actions"
> color sel gold
No statusbar messages will be shown due to inadequate OpenGL
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
> color sel blue
> color sel light gray
> color sel hot pink
> ui tool show "Segment Map"
Segmenting j71_flip.mrc, density threshold 0.358920
Showing j71_flip.seg - 0 regions, 0 surfaces
Only showing 60 of 109 regions.
Showing 60 of 109 region surfaces
1846 watershed regions, grouped to 109 regions
> select #3
61 models selected
> transparency #3 30
> hide #!1 models
Drag select of 2614, 19 of 56720 triangles, 2623, 4363 of 28848 triangles,
2656, 2911 of 26576 triangles, 2628, 15194 of 20364 triangles, 2651, 201 of
19284 triangles, 2507, 13978 of 16356 triangles, 2509, 1867 of 14084
triangles, 2647, 11223 of 13292 triangles, 2496, 8511 of 12016 triangles,
2613, 4783 of 12708 triangles, 2588, 6457 of 12336 triangles, 2539, 1151 of
9596 triangles, 2569, 46 of 9540 triangles, 2652, 3306 of 9676 triangles,
2636, 1049 of 10120 triangles, 2640, 242 of 10032 triangles, 2626, 320 of 8600
triangles, 2489, 4764 of 9084 triangles, 2635, 3056 of 7316 triangles, 2638,
4276 of 5540 triangles, 2487, 3684 of 6300 triangles, 2589, 3448 of 5224
triangles, 2529, 1396 of 6012 triangles, 2519, 178 atoms, 191 residues, 10
pseudobonds, 179 bonds
Grouped 24 regions
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
Ungrouped to 62 regions, but did not show all surfaces, see Options
Ungrouped to 123 regions, but did not show all surfaces, see Options
Ungrouped to 92 regions, but did not show all surfaces, see Options
Ungrouped to 23 regions, but did not show their surfaces, see Options
Ungrouped to 125 regions, but did not show all surfaces, see Options
Ungrouped to 400 regions, but did not show all surfaces, see Options
Ungrouped to 1039 regions, but did not show all surfaces, see Options
Ungrouped to 710 regions, but did not show their surfaces, see Options
Ungrouped to 0 regions, but did not show their surfaces, see Options
Ungrouped to 0 regions, but did not show their surfaces, see Options
Ungrouped to 0 regions, but did not show their surfaces, see Options
Ungrouped to 0 regions, but did not show their surfaces, see Options
Ungrouped to 0 regions, but did not show their surfaces, see Options
> close #3
No visible Surface models
> select
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 5 models selected
> transparency (#!2 & sel) 30
> surface (#!2 & sel)
> hide #1.1 models
> ui tool show "Color Actions"
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 2
> color (#!2 & sel) cornflower blue
> color (#!2 & sel) yellow
> ui tool show "Color Actions"
> color sel gold
> color sel orange
> color (#!2 & sel) blue
> ui tool show "Color Actions"
> color sel violet
> color sel plum
> select /A
5095 atoms, 5227 bonds, 28 pseudobonds, 622 residues, 3 models selected
> select /C
5095 atoms, 5227 bonds, 28 pseudobonds, 622 residues, 3 models selected
> surface hidePatches (#!2 & sel)
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
> color (#!2 & sel) light gray
> transparency (#!2 & sel) 40
> select clear
> select /A
5095 atoms, 5227 bonds, 28 pseudobonds, 622 residues, 3 models selected
> transparency (#!2 & sel) 30
> select /C
5095 atoms, 5227 bonds, 28 pseudobonds, 622 residues, 3 models selected
> surface (#!2 & sel)
> cartoon (#!2 & sel)
> select /C:274@CA
1 atom, 1 residue, 1 model selected
Drag select of EGTA-f_real_space_refined-coot-2_sequence corrected.pdb_C SES
surface, 37450 of 577352 triangles, 52 residues
> select clear
> select
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 5 models selected
> transparency (#!2 & sel) 30
> save "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/NOX5_MS/NOX5_final_figures/Nox5_color_chimeraX_surface.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/NOX5_MS/NOX5_final_figures/1.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> select
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 5 models selected
> transparency (#!2 & sel) 60
> cartoon hide (#!2 & sel)
> hide (#!2 & sel) target a
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 1 model selected
> show sel target ab
> select ::name="NDP"
96 atoms, 104 bonds, 2 residues, 1 model selected
> show sel target ab
> select /A
5095 atoms, 5227 bonds, 28 pseudobonds, 622 residues, 3 models selected
> hide (#!2 & sel) target a
> select clear
> select ::name="HEB"
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> show (#!2 & sel) target ab
> select /A
5095 atoms, 5227 bonds, 28 pseudobonds, 622 residues, 3 models selected
> hide (#!2 & sel) target a
> select clear
> select
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 5 models selected
> transparency (#!2 & sel) 80
> select clear
> select ::name="CYS"
180 atoms, 152 bonds, 30 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> surface (#!2 & sel)
> select /C:246@CB
1 atom, 1 residue, 1 model selected
> show (#!2 & sel) target ab
> cartoon (#!2 & sel)
> show (#!2 & sel-residues & sidechain) target ab
> select clear
> select
10190 atoms, 10454 bonds, 56 pseudobonds, 1244 residues, 5 models selected
> surface (#!2 & sel)
> select ::name="CYS"
180 atoms, 152 bonds, 30 residues, 1 model selected
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
> cartoon (#!2 & sel)
> cartoon hide (#!2 & sel)
> select clear
> cartoon #2
> cartoon hide #2
> hide #2.4 models
> show #2.4 models
> hide #2.3 models
> show #2.3 models
> hide #!2 models
> show #!2 models
> cartoon #2
> hide #2.3 models
> hide #2.4 models
> select /C:235
6 atoms, 5 bonds, 1 residue, 1 model selected
> show (#!2 & sel) target ab
> color (#!2 & sel) byelement
> select clear
> surface #2.1-2#!2
> cartoon hide #2
> select /C:274@CB
1 atom, 1 residue, 1 model selected
> cartoon (#!2 & sel)
> cartoon hide (#!2 & sel)
> select clear
> cartoon #2
> select /C:278@CG
1 atom, 1 residue, 1 model selected
> select /C:278@CD2
1 atom, 1 residue, 1 model selected
> surface hidePatches (#!2 & sel)
> surface (#!2 & sel)
> select clear
> select /C:235@SG
1 atom, 1 residue, 1 model selected
> select ~sel
9918 atoms, 10180 bonds, 56 pseudobonds, 1206 residues, 5 models selected
> cartoon hide (#!2 & sel)
> surface (#!2 & sel)
> select ~sel
272 atoms, 274 bonds, 38 residues, 1 model selected
> surface (#!2 & sel)
> select ~sel
9918 atoms, 10180 bonds, 56 pseudobonds, 1206 residues, 5 models selected
> select clear
> surface #2
> cartoon hide (#!2 & sel)
> select /A
5095 atoms, 5227 bonds, 28 pseudobonds, 622 residues, 3 models selected
> cartoon hide (#!2 & sel)
> select clear
> cartoon (#!2 & sel)
> select /A
5095 atoms, 5227 bonds, 28 pseudobonds, 622 residues, 3 models selected
> cartoon hide (#!2 & sel)
> select /C:251@O
1 atom, 1 residue, 1 model selected
> select ::name="HEB"
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> color (#!2 & sel) byelement
> ui tool show "Color Actions"
> color sel byelement
> select clear
> save "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/NOX5_MS/NOX5_final_figures/Ligand_on_surface.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/NOX5_MS/NOX5_final_figures/ligand.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> close #1
> hide #2.4 models
> show #2.4 models
> hide #2.3 models
> show #2.3 models
> save "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/NOX5_MS/NOX5_final_figures/ligand.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "C:/Users/njain04/OneDrive - St. Jude Children's Research
> Hospital/NOX5_MS/NOX5_final_figures/ligaND.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1290, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 158, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 327, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000016354D5B948> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x0000016308F6F788> ->
<chimerax.segger.fit_dialog.Fit object at 0x0000016309EE18C8> ->
<chimerax.atomic.structure.AtomicStructure object at 0x0000016308BC2088>
'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save
mgr).save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb':
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x0000016354D5B948> -> <chimerax.segger.fit_dialog.FitSegmentsDialog
object at 0x0000016308F6F788> -> <chimerax.segger.fit_dialog.Fit object at
0x0000016309EE18C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x0000016308BC2088> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
ValueError: error processing: 'tools' -> -> -> -> 'EGTA-f_real_space_refined-
coot-2_sequence corrected.pdb': Error while saving session data for 'tools' ->
-> -> -> 'EGTA-f_real_space_refined-coot-2_sequence corrected.pdb'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.8681
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 7410
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 16,827,981,824
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10810U CPU @ 1.10GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Structure positions is None (Segger holding ref to dead Structure) |
comment:2 by , 4 years ago
| Cc: | added |
|---|---|
| Resolution: | → fixed |
| Status: | assigned → closed |
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Fixed in tomorrow's daily build.
The ChimeraX error saving a session was because the a molecule fit to a segmentation with Fit to Segments dialog had been deleted. The session save code mistakenly tried to save the deleted molecule. I made it ignore deleted molecules.
If you run into this again you can get around the problem using Fit to Segments panel menu entry Fit / Delete Selected Fits From List or Fit / Delete ALL Fits from List in order to delete the fit involving the deleted molecule. Then session save will work.