Opened 6 years ago

Closed 3 years ago

#2374 closed defect (fixed)

ISOLDE: multiple different errors

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> open
/net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/shlth_1_rsr3-coot-3.pdb

Summary of feedback from opening
/net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/shlth_1_rsr3-coot-3.pdb  
---  
warnings | Ignored bad PDB record found on line 47  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 48  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 49  
BOND : 0.006 0.072 7064  
  
Ignored bad PDB record found on line 50  
ANGLE : 1.617 53.274 12727  
  
Ignored bad PDB record found on line 51  
CHIRALITY : 0.063 0.479 593  
  
16 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 ALA 83 PHE 90 1 8  
Start residue of secondary structure not found: HELIX 2 2 GLN 95 ASN 101 1 7  
Start residue of secondary structure not found: HELIX 3 3 PHE 103 PHE 104 1 2  
Start residue of secondary structure not found: HELIX 4 4 ILE 147 LEU 150 1 4  
Start residue of secondary structure not found: HELIX 6 6 ILE 260 VAL 267 1 8  
13 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 D 2 ALA 152 ILE 160 0  
Start residue of secondary structure not found: SHEET 2 D 2 VAL 170 PHE 175 -1  
Start residue of secondary structure not found: SHEET 1 E 2 ALA 196 SER 199 0  
Start residue of secondary structure not found: SHEET 2 E 2 LYS 206 SER 209 -1  
Start residue of secondary structure not found: SHEET 1 F 2 TYR 298 PHE 301 0  
Start residue of secondary structure not found: SHEET 2 F 2 ARG 326 LEU 329 1  
6 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 6 6 ILE 229 ALA 231 1 3  
Start residue of secondary structure not found: HELIX 7 7 LEU 257 VAL 267 1 11  
Start residue of secondary structure not found: HELIX 8 8 ASP 280 ALA 292 1 13  
Start residue of secondary structure not found: HELIX 9 9 THR 303 TYR 305 1 3  
Start residue of secondary structure not found: HELIX 10 10 PRO 313 LYS 318 1
6  
Start residue of secondary structure not found: HELIX 11 11 ARG 335 TYR 341 1
7  
14 messages similar to the above omitted  
  
Chain information for shlth_1_rsr3-coot-3.pdb #1  
---  
Chain | Description  
| No description available  
  

> open /net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/x1_shlth2.mrc

Opened x1_shlth2.mrc, grid size 60,72,56, pixel 1.62,1.62,1.62, shown at level
2.71, step 1, values float32  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> select #1

7159 atoms, 7170 bonds selected  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for shlth_1_rsr3-coot-3.pdb  
---  
Chain | Description  
1.3/  | No description available  
  
Done loading forcefield  
/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/molobject.py:1720: RuntimeWarning: divide by zero
encountered in double_scalars  
self.global_k = scaling_constant/ref_g  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Doing nothing  

> style selAtoms stick

Changed 7159 atom styles  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode select

> ui mousemode rightMode rotate

Bad residue number: 1  
Doing nothing  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands: surf hide; style
(protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh
def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20;
cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x
rect; nucleotides tube/slab shape box  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> toolshed show "Basic Actions"

> open /net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/x1_shlth2.mrc

Opened x1_shlth2.mrc, grid size 60,72,56, pixel 1.62,1.62,1.62, shown at level
2.71, step 1, values float32  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> hide #!2 models

> hide #!2.1 models

> show #!2 models

> show #!2.1 models

> select

7159 atoms, 7170 bonds, 18 models selected  

> select clear

> select

7159 atoms, 7170 bonds, 18 models selected  

> select clear

> color selAtoms bychain

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> select clear

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode pivot

> ui mousemode rightMode "rotate selected models"

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> fitmap #1 inMap #2

Fit molecule shlth_1_rsr3-coot-3.pdb (#1.3) to map x1_shlth2.mrc (#2) using
7159 atoms  
average map value = 1.49, steps = 160  
shifted from previous position = 8.82  
rotated from previous position = 41.3 degrees  
atoms outside contour = 5245, contour level = 2.443  
  
Position of shlth_1_rsr3-coot-3.pdb (#1.3) relative to x1_shlth2.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99999717 0.00108140 -0.00211750 -16.30497335  
-0.00106877 0.99998170 0.00595530 30.58341123  
0.00212390 -0.00595302 0.99998003 -46.80005943  
Axis -0.92869285 -0.33077367 -0.16768534  
Axis point 0.00000000 -7479.22200823 -5873.52545832  
Rotation angle (degrees) 0.36734513  
Shift along axis 12.87380853  
  

> fitmap #1 inMap #2

Fit molecule shlth_1_rsr3-coot-3.pdb (#1.3) to map x1_shlth2.mrc (#2) using
7159 atoms  
average map value = 1.49, steps = 112  
shifted from previous position = 2.08  
rotated from previous position = 13.5 degrees  
atoms outside contour = 3904, contour level = 1.2605  
  
Position of shlth_1_rsr3-coot-3.pdb (#1.3) relative to x1_shlth2.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99999733 0.00103974 -0.00206562 -16.30158009  
-0.00102773 0.99998262 0.00580558 30.57565674  
0.00207162 -0.00580344 0.99998101 -46.81007184  
Axis -0.92898752 -0.33107437 -0.16544469  
Axis point 0.00000000 -7682.30388464 -6017.57961543  
Rotation angle (degrees) 0.35799862  
Shift along axis 12.76562638  
  

> ui mousemode rightMode zoom

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> select #1

7159 atoms, 7170 bonds, 16 models selected  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> select #1

7159 atoms, 7170 bonds, 16 models selected  

> select #1

7159 atoms, 7170 bonds, 16 models selected  

> select #1

7159 atoms, 7170 bonds, 16 models selected  

> select #1

7159 atoms, 7170 bonds, 16 models selected  

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

Bad residue number: 1  
Doing nothing  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 1  
Excluding residue  
Bad residue number: 2  
Excluding residue  
Bad residue number: 2  
Excluding residue  
Bad residue number: 26  
Excluding residue  
Bad residue number: 47  
Excluding residue  
Bad residue number: 47  
Excluding residue  
Bad residue number: 47  
Excluding residue  
Bad residue number: 49  
Excluding residue  
Bad residue number: 49  
Excluding residue  
Bad residue number: 49  
Excluding residue  
Bad residue number: 49  
Excluding residue  
Bad residue number: 49  
Excluding residue  
Bad residue number: 50  
Excluding residue  
Bad residue number: 50  
Excluding residue  
Bad residue number: 138  
Excluding residue  
Bad residue number: 138  
Excluding residue  
Bad residue number: 138  
Excluding residue  
Bad residue number: 141  
Excluding residue  
Bad residue number: 141  
Excluding residue  
Bad residue number: 142  
Excluding residue  
Bad residue number: 149  
Excluding residue  
Bad residue number: 75  
Excluding residue  
Bad residue number: 202  
Excluding residue  
Bad residue number: 222  
Excluding residue  
Bad residue number: 241  
Excluding residue  

> hide #!2 models

Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 445, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/tugging.py", line 103, in mouse_down  
pick = picking.pick_closest_to_line(self.session, x, y, self._atoms, 0.5)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/picking.py", line 25, in pick_closest_to_line  
length = numpy.linalg.norm(xyz2-xyz1)  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/picking.py", line 25, in pick_closest_to_line  
length = numpy.linalg.norm(xyz2-xyz1)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 445, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/tugging.py", line 103, in mouse_down  
pick = picking.pick_closest_to_line(self.session, x, y, self._atoms, 0.5)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/picking.py", line 25, in pick_closest_to_line  
length = numpy.linalg.norm(xyz2-xyz1)  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/picking.py", line 25, in pick_closest_to_line  
length = numpy.linalg.norm(xyz2-xyz1)  
  
See log for complete Python traceback.  
  

> hide #!2 models

> show #!2 models

> select #2

4 models selected  

> ~select #2

Nothing selected  

> ~select #1

Nothing selected  

> select #1

7159 atoms, 7170 bonds, 16 models selected  
Exception ignored in: <function Buffer.__del__ at 0x1550f902ed08>  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2393, in __del__  
% self.shader_variable_name)  
RuntimeError: OpenGL buffer "None" was not deleted before core.graphics.Buffer
destroyed  

> select #1

7159 atoms, 7170 bonds, 16 models selected  
Exception ignored in: <function Buffer.__del__ at 0x1550f902ed08>  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2393, in __del__  
% self.shader_variable_name)  
RuntimeError: OpenGL buffer "None" was not deleted before core.graphics.Buffer
destroyed  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 445, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/tugging.py", line 103, in mouse_down  
pick = picking.pick_closest_to_line(self.session, x, y, self._atoms, 0.5)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/picking.py", line 25, in pick_closest_to_line  
length = numpy.linalg.norm(xyz2-xyz1)  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/picking.py", line 25, in pick_closest_to_line  
length = numpy.linalg.norm(xyz2-xyz1)  
  
See log for complete Python traceback.  
  

> select #1.1

6 models selected  

> select #1.2

2 models selected  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

QWidget::repaint: Recursive repaint detected  

> clipper spotlight radius 11.00

Setting spotlight mode for model 1.3 to True  

> clipper spotlight radius 10.00

Setting spotlight mode for model 1.3 to True  

> clipper spotlight radius 9.00

Setting spotlight mode for model 1.3 to True  

> clipper spotlight radius 10.00

Setting spotlight mode for model 1.3 to True  

> clipper spotlight radius 11.00

Setting spotlight mode for model 1.3 to True  

> select #1.2

2 models selected  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  

> show #1.3 target m

> show selAtoms ribbons

> fitmap #1 inMap #2

Fit molecule shlth_1_rsr3-coot-3.pdb (#1.3) to map x1_shlth2.mrc (#2) using
7159 atoms  
average map value = 1.48, steps = 60  
shifted from previous position = 0.0168  
rotated from previous position = 0.00891 degrees  
atoms outside contour = 3392, contour level = 0.8534  
  
Position of shlth_1_rsr3-coot-3.pdb (#1.3) relative to x1_shlth2.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99999699 0.00109272 -0.00219547 -16.30879867  
-0.00108011 0.99998295 0.00573836 30.58324907  
0.00220170 -0.00573597 0.99998113 -46.83312006  
Axis -0.91951761 -0.35237497 -0.17412421  
Axis point 0.00000000 -7769.05475207 -6112.55687240  
Rotation angle (degrees) 0.35748923  
Shift along axis 12.37423620  
  

> fitmap #1 inMap #2

Fit molecule shlth_1_rsr3-coot-3.pdb (#1.3) to map x1_shlth2.mrc (#2) using
7159 atoms  
average map value = 1.48, steps = 48  
shifted from previous position = 0.00955  
rotated from previous position = 0.0104 degrees  
atoms outside contour = 3391, contour level = 0.8534  
  
Position of shlth_1_rsr3-coot-3.pdb (#1.3) relative to x1_shlth2.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99999706 0.00116182 -0.00212953 -16.32220427  
-0.00114991 0.99998374 0.00558507 30.58776689  
0.00213598 -0.00558261 0.99998214 -46.84164871  
Axis -0.91718540 -0.35032051 -0.18985912  
Axis point 0.00000000 -7923.24146483 -6324.48234943  
Rotation angle (degrees) 0.34881982  
Shift along axis 13.14827934  
  

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> toolshed show "Model Panel"

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> toolshed show "Modeller Comparative"

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> select #2

4 models selected  
Traceback (most recent call last):  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 2647, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 2664, in start_sim  
main_sel = self._last_main_sel = self._get_main_sim_selection()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 2811, in _get_main_sim_selection  
raise TypeError('You must select at least one atom from the current '  
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!  
  
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 2811, in _get_main_sim_selection  
raise TypeError('You must select at least one atom from the current '  
  
See log for complete Python traceback.  
  

> select #1.3

7159 atoms, 7170 bonds, 10 models selected  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 273, in
_model_changed_cb  
self.update_scatter()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 370, in update_scatter  
if not self.visible:  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 281, in visible  
return self.parent.isVisible()  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes": wrapped C/C++ object of type QVBoxLayout
has been deleted:  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/validation/ramaplot.py", line 277, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 390.77
OpenGL renderer: GeForce GTX 1060 6GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: multiple different errors

comment:2 by Tristan Croll, 6 years ago

Well, that log tells a strange story:

Error the first: looks like the user linked map and model for ISOLDE before the model was actually docked into the map. Since ISOLDE uses the map gradients in the region directly surrounding the model to choose a suitable force constant for map fitting, it's come out with NaN since there are no voxels nearby. I guess I can add some code to catch this scenario and warn the user.

Error the second: the string of "Bad residue number: ..." log entries. Each of these is a residue with a topology not found in the MD forcefield. The sheer number of them first led me to suspect that the user simply hasn't added hydrogens, and is not reading the instructions in the dialog box that pops up every time - simply choosing to ignore each offending residue in turn. In any case, the log suggests that at least the first *21* residues in the model had wrong topology. A few candidates here (apart from missing hydrogens) are missing backbone atoms, prolines truncated to alanine (not supported on purpose - doing that is asking for trouble), or simply something exotic. I should improve the log message given in these cases to at least give the residue name to aid in diagnosis.

Error the third: the user's closed the ISOLDE GUI with a simulation still running. That's the same as #2204. I'll bump up the urgency on working out how to safely catch that scenario.

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed
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