Opened 4 years ago

Closed 4 years ago

#5277 closed defect (duplicate)

ISOLDE: various dead widgets being accessed

Reported by: sremm@… 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-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I get this kind of error messages when I try to choose better rotamers using ISOLDE

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> open 1a0m structureFactors true

Summary of feedback from opening 1a0m fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 473 free from 9265 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 1.0944213038232693  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 72,72,74, pixel
0.347,0.347,0.326, shown at level 2.46, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 72,72,74, pixel
0.347,0.347,0.326, shown at level -0.302,0.302, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_27 as #1.1.1.4, grid size 72,72,74, pixel
0.347,0.347,0.326, shown at level 0.906, step 1, values float32  
1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m  
---  
Chain | Description  
1.2/A 1.2/B | α-conotoxin [TYR15]-epi  
  
Non-standard residues in 1a0m #1.2  
---  
NH2 — amino group  
  

> save /home/centos/Desktop/1a0m.mtz #1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  

> set bgColor white

> ui tool show ISOLDE

> set selectionWidth 4

Opened (LIVE) MDFF potential as #1.1.1.5, grid size 72,72,74, pixel
0.347,0.347,0.326, shown at level 0.921, step 1, values float32  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to 1a0m #1.2  
---  
warning | Not adding hydrogens to /A ARG 7 CB because it is missing heavy-atom
bond partners  
notes | Termini for 1a0m (#1.2) chain A determined from SEQRES records  
Termini for 1a0m (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLY 1, /B GLY 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A NH2 17, /B NH2 17  
Chain-final residues that are not actual C termini:  
107 hydrogen bonds  
271 hydrogens added  
  

> hide HC

> select #1

547 atoms, 513 bonds, 76 residues, 24 models selected  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  

> select #1

547 atoms, 513 bonds, 76 residues, 30 models selected  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> select #1

547 atoms, 513 bonds, 76 residues, 30 models selected  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select #1

547 atoms, 513 bonds, 76 residues, 30 models selected  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> select #1

547 atoms, 513 bonds, 76 residues, 30 models selected  
ISOLDE: started sim  

> select #1

547 atoms, 513 bonds, 76 residues, 30 models selected  
reverting to start  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
ISOLDE: started sim  
reverting to start  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select #1

547 atoms, 513 bonds, 76 residues, 30 models selected  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
ISOLDE: started sim  
reverting to start  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> close #1

Deleting Crystallographic maps (1a0m-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_27  
Deleting (LIVE) MDFF potential  

> isolde demo crystal_intro

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
1.2/A | predicted microcompartment protein  
  

WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at
level 0.302, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at
level -0.0582,0.0582, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723,
shown at level 0.603, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723,
shown at level 0.365, step 1, values float32  
Loaded crystallographic demo: PDB ID 3io0  

QXcbClipboard: SelectionRequest too old  

QXcbClipboard: SelectionRequest too old  

> cview /A:187

> isolde sim start #1

ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> select #1

3348 atoms, 3371 bonds, 229 residues, 30 models selected  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> select up

160 atoms, 161 bonds, 12 residues, 1 model selected  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> hbonds #1

205 hydrogen bonds found  

QXcbClipboard: SelectionRequest too old  

QXcbClipboard: SelectionRequest too old  

> ~hbonds

> close #1

Deleting Crystallographic maps (3io0-sf.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) MDFF potential  
'NoneType' object has no attribute 'triggers'  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> open /mnt/processing/sremm/13.1_refine_17_60.mtz
> /mnt/processing/sremm/13.1_refine_17_60.pdb

Must specify a structure model to associate with crystallographic data  

> open /mnt/processing/sremm/13.1_refine_17_60.pdb

Chain information for 13.1_refine_17_60.pdb #1  
---  
Chain | Description  
A | No description available  
B D | No description available  
C | No description available  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
  
See log for complete Python traceback.  
  
Chain information for 13.1_refine_17_60.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B 1.2/D | No description available  
1.2/C | No description available  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

> open /mnt/processing/sremm/13.1_refine_17_60.mtz

Must specify a structure model to associate with crystallographic data  

> open /mnt/processing/sremm/13.1_refine_17_60.mtz

Must specify a structure model to associate with crystallographic data  

> open /mnt/processing/sremm/13.1_refine_17_60.mtz

Must specify a structure model to associate with crystallographic data  
Opened (STATIC) (Model-structure-factors-(bulk-solvent-and-all-scales-
included)) F-model, PHIF-model as #1.1.1.2, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level -0.337,0.337, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.3,
grid size 54,38,40, pixel 0.642,0.669,0.647, shown at level 0.199, step 1,
values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.4, grid size 54,38,40, pixel 0.642,0.669,0.647, shown at level
0.186, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.5, grid
size 54,38,40, pixel 0.642,0.669,0.647, shown at level -0.177,0.177, step 1,
values float32  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  

> close #1

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
  
See log for complete Python traceback.  
  
Deleting Crystallographic maps (13.1_refine_17_60.mtz)  

> open /mnt/processing/sremm/13.1_refine_17_ISOLDE/13.1_refine_17_60.pdb

Chain information for 13.1_refine_17_60.pdb #1  
---  
Chain | Description  
A | No description available  
B D | No description available  
C | No description available  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
  
See log for complete Python traceback.  
  
Chain information for 13.1_refine_17_60.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B 1.2/D | No description available  
1.2/C | No description available  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1013, in
_update_model_list  
mmcb.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

WARNING: found column "/crystal/dataset/K_ISOTROPIC F" suggesting one of the
data types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following
column type "F" does not match any of the expected types (Q, P). Importing of
this column has been skipped.  

WARNING: found column "/crystal/dataset/K_ANISOTROPIC F" suggesting one of the
data types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following
column type "F" does not match any of the expected types (Q, P). Importing of
this column has been skipped.  

WARNING: found column "/crystal/dataset/FOM F" suggesting one of the data
types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following column
type "F" does not match any of the expected types (Q, P). Importing of this
column has been skipped.  

WARNING: found column "/crystal/dataset/ALPHA F" suggesting one of the data
types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following column
type "F" does not match any of the expected types (Q, P). Importing of this
column has been skipped.  

WARNING: found column "/crystal/dataset/BETA F" suggesting one of the data
types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following column
type "A" does not match any of the expected types (Q, P). Importing of this
column has been skipped.  

Discarding unrecognised/unsupported data array /crystal/dataset/HLmodelA A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLmodelB A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLmodelC A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLmodelD A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLcombA A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLcombB A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLcombC A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLcombD A  
Discarding unrecognised/unsupported data array /crystal/dataset/RESOLUTION R  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level 0.194, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level -0.0876,0.0876, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_18 as #1.1.1.4, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level 0.339, step 1, values float32  
Opened (STATIC) (dataset) FMODEL, PHIFMODEL as #1.1.1.5, grid size 54,38,40,
pixel 0.642,0.669,0.647, shown at level -0.64,0.64, step 1, values float32  
Opened (STATIC) (dataset) FCALC, PHIFCALC as #1.1.1.6, grid size 54,38,40,
pixel 0.642,0.669,0.647, shown at level -0.544,0.544, step 1, values float32  
Opened (STATIC) (dataset) FMASK, PHIFMASK as #1.1.1.7, grid size 54,38,40,
pixel 0.642,0.669,0.647, shown at level -1.19,1.19, step 1, values float32  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level 0.185, step 1, values float32  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  

> close #1.1.1

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Deleting Crystallographic maps (13_fmodel.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_18  
Deleting (LIVE) MDFF potential  
Opened (STATIC) (dataset) 2FOFCWT, PH2FOFCWT as #1.1.1.2, grid size 54,38,40,
pixel 0.642,0.669,0.647, shown at level 0.194, step 1, values float32  
Opened (STATIC) (dataset) 2FOFCWT_sharp, PH2FOFCWT_sharp as #1.1.1.3, grid
size 54,38,40, pixel 0.642,0.669,0.647, shown at level 0.423, step 1, values
float32  
Opened (STATIC) (dataset) FOFCWT, PHFOFCWT as #1.1.1.4, grid size 54,38,40,
pixel 0.642,0.669,0.647, shown at level -0.173,0.173, step 1, values float32  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  

> close #1.1.1

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Deleting Crystallographic maps (13_map_coeffs.mtz)  

WARNING: found column "/crystal/dataset/K_ISOTROPIC F" suggesting one of the
data types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following
column type "F" does not match any of the expected types (Q, P). Importing of
this column has been skipped.  

WARNING: found column "/crystal/dataset/K_ANISOTROPIC F" suggesting one of the
data types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following
column type "F" does not match any of the expected types (Q, P). Importing of
this column has been skipped.  

WARNING: found column "/crystal/dataset/FOM F" suggesting one of the data
types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following column
type "F" does not match any of the expected types (Q, P). Importing of this
column has been skipped.  

WARNING: found column "/crystal/dataset/ALPHA F" suggesting one of the data
types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following column
type "F" does not match any of the expected types (Q, P). Importing of this
column has been skipped.  

WARNING: found column "/crystal/dataset/BETA F" suggesting one of the data
types (HKL_data_F_sigF_float, HKL_data_F_phi_float), but the following column
type "A" does not match any of the expected types (Q, P). Importing of this
column has been skipped.  

Discarding unrecognised/unsupported data array /crystal/dataset/HLmodelA A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLmodelB A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLmodelC A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLmodelD A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLcombA A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLcombB A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLcombC A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLcombD A  
Discarding unrecognised/unsupported data array /crystal/dataset/RESOLUTION R  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level 0.195, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level -0.0881,0.0881, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_18 as #1.1.1.4, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level 0.341, step 1, values float32  
Opened (STATIC) (dataset) FMODEL, PHIFMODEL as #1.1.1.5, grid size 54,38,40,
pixel 0.642,0.669,0.647, shown at level -0.64,0.64, step 1, values float32  
Opened (STATIC) (dataset) FCALC, PHIFCALC as #1.1.1.6, grid size 54,38,40,
pixel 0.642,0.669,0.647, shown at level -0.544,0.544, step 1, values float32  
Opened (STATIC) (dataset) FMASK, PHIFMASK as #1.1.1.7, grid size 54,38,40,
pixel 0.642,0.669,0.647, shown at level -1.19,1.19, step 1, values float32  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 54,38,40, pixel
0.642,0.669,0.647, shown at level 0.185, step 1, values float32  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1041, in
_update_model_list  
self._populate_available_volumes_combo_box()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1471, in
_populate_available_volumes_combo_box  
cb.clear()  
  
See log for complete Python traceback.  
  

> addh

Summary of feedback from adding hydrogens to 13.1_refine_17_60.pdb #1.2  
---  
notes | No usable SEQRES records for 13.1_refine_17_60.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for 13.1_refine_17_60.pdb (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for 13.1_refine_17_60.pdb (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for 13.1_refine_17_60.pdb (#1.2) chain D; guessing
termini instead  
Chain-initial residues that are actual N termini: /A THR 16, /B GLN 1, /C THR
16, /D GLN 1  
Chain-initial residues that are not actual N termini: /C ASN 55  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ARG 512, /B VAL 116, /C
ALA 509, /C MET 47, /D VAL 116  
973 hydrogen bonds  
Adding 'H' to /C ASN 55  
/A ARG 512 is not terminus, removing H atom from 'C'  
/B VAL 116 is not terminus, removing H atom from 'C'  
/C ALA 509 is not terminus, removing H atom from 'C'  
/D VAL 116 is not terminus, removing H atom from 'C'  
9415 hydrogens added  
  

> hide HC

> hide HC

> select #1

18457 atoms, 18642 bonds, 1 pseudobond, 1216 residues, 38 models selected  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> select #1

18457 atoms, 18642 bonds, 1 pseudobond, 1216 residues, 44 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 1044, in
_update_model_list  
self._change_selected_model(model=current_model)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2478, in
_change_selected_model  
self._update_iffy_rota_list()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2389, in
_update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.73.01
OpenGL renderer: Tesla T4/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: OpenStack Foundation
Model: OpenStack Nova
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: kvm
CPU: 128 AMD EPYC 7702 64-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           478G         53G         50G        240M        374G        422G
	Swap:            0B          0B          0B

Graphics:
	unknown
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: various dead widgets being accessed

Reported by Sille Remm

comment:2 by Tristan Croll, 4 years ago

Resolution: → duplicate
Status: assigned → closed

See my response to #5282 - for now, this can be avoided by not closing and reopening the ISOLDE panel within the same ChimeraX session.

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