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#5282 closed defect (can't reproduce)

Ramachandran plot clashes: wrapped C/C++ object of type QComboBox has been deleted

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 (last modified by pett)

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
ISOLDE simulation was running and a protein loop seemed to be clashing with the symmetry mate. The error occurred when I had hid the Ramachandran plot and clicked on the "Clashes" tab to see what it said there about this clash. The error message would not close, although simulation seemed to run on normally.

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

> open
> /mnt/processing/sremm/13.1_refine_17_ISOLDE/13.1_refine_17_ISOLDE_1_mainsim.cxs

restore_snapshot for "RotamerRestraintMgr" returned None  

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 1,1,1, pixel 0.642,0.669,0.647,
shown at level 0.196, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 1,1,1, pixel 0.642,0.669,0.647,
shown at level -0.0883,0.0883, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_18 as #1.1.1.4, grid size 1,1,1, pixel
0.642,0.669,0.647, shown at level 0.341, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 1,1,1, pixel
0.642,0.669,0.647, shown at level 0.186, step 1, values float32  
Restoring stepper: 13.1_refine_17_60.pdb  
Log from Thu Sep 23 13:33:26 2021UCSF 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.  
  
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.  
  

> 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  

> close #1.2

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)  
  

[many of these deleted]

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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
See log for complete Python traceback.  
  
reverting to start  
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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
  
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         49G         54G        167M        374G        426G
	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 (3)

comment:1 by pett, 4 years ago

Component:	Unassigned → Third Party
Description:	modified (diff)
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Ramachandran plot clashes: wrapped C/C++ object of type QComboBox has been deleted

comment:2 by Tristan Croll, 4 years ago

Status:	assigned → feedback

The initial string of errors is due to my failure to clean up some callbacks on closing ISOLDE - that causes problems when you close it and then launch a new ISOLDE instance in the same session (something I don't do myself, so I never noticed the issue until bug reports came in). I think I've gotten all of those now... but there's a completely different error filling the tail end of the log, relating to the last dataset you were working on:

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/clipper/delayed_reaction.py",
line 52, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
Error processing trigger "new frame":  
RuntimeError: Xmap: Internal map ASU error - P 2yb Nuvw = ( 72, 180, 96)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/clipper/maps/xmapset.py", line
718, in _apply_new_maps  
xm.apply_new_maps()

That's something a bit more concerning. Is there any chance you could share (by direct email to tic20@… if you prefer) a copy of that model and MTZ to help me diagnose? I will of course keep it confidential if you require it.

comment:3 by Tristan Croll, 4 years ago

Resolution:	→ can't reproduce
Status:	feedback → closed

Thank you very much for sharing the model and structure factors. Unfortunately I haven't been able to reproduce that Xmap traceback, so it's probably going to remain a mystery unless it comes up again.

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