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Opened 6 years ago
Closed 3 years ago
#2531 closed defect (fixed)
"spotlight moved" trigger handler using dead Structure
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-957.21.3.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-10-10)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.91 (2019-10-10)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
/nfs4/suffolk/WorkComplexIC/anaa2/20190412w1118DmcomplexI/model_building/working/1_Isolde_chains_working/B/chainB_working1.pdb
chainB_working1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6g72.1
[more info...]
Chain information for chainB_working1.pdb #1
---
Chain | Description
B | No description available
Non-standard residues in chainB_working1.pdb #1
---
SF4 — (SF4)
> set bgColor white
> open
/nfs4/suffolk/WorkComplexIC/anaa2/20190412w1118DmcomplexI/model_building/1_inital_maps/3_3_angstroms/postprocess_job591.mrc
Opened postprocess_job591.mrc, grid size 450,450,450, pixel 1.05, shown at
level 0.00849, step 2, values float32
> isolde start
> set selectionWidth 4
chainB_working1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6g72.1
[more info...]
Chain information for chainB_working1.pdb
---
Chain | Description
1.3/B | No description available
Non-standard residues in chainB_working1.pdb #1.3
---
SF4 — (SF4)
Done loading forcefield
> clipper spotlight radius 11.00
Setting spotlight mode for model 1.3 to True
> clipper spotlight radius 9.00
Setting spotlight mode for model 1.3 to True
> clipper spotlight radius 25.00
Setting spotlight mode for model 1.3 to True
> select :SF4
8 atoms, 18 pseudobonds, 2 models selected
> toolshed show Shell
/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
6 atoms were automatically renamed to match the template: S3->S2, FE4->FE3,
FE2->FE4, FE3->FE2, S4->S3, S2->S4
> select clear
> sequence chain /B
Alignment identifier is 1.3.B
Bad residue number: match
Adding hydrogens
Summary of feedback from adding hydrogens to chainB_working1.pdb #1.3
---
notes | No usable SEQRES records for chainB_working1.pdb (#1.3) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: /B GLN 17
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /B LYS 198
Chain-final residues that are not actual C termini:
107 hydrogen bonds
1453 hydrogens added
> select clear
> hide HC
> view sel
> cofr centerOfView
> select clear
> select clear
> select clear
> view sel
> cofr centerOfView
> view sel
> cofr centerOfView
> select clear
> view sel
> cofr centerOfView
> graphics silhouettes true
> view sel
> cofr centerOfView
> select clear
> select clear
> view sel
> cofr centerOfView
> view sel
> cofr centerOfView
> select clear
> select clear
> view sel
> cofr centerOfView
> select clear
> select clear
> view sel
> cofr centerOfView
> view sel
> cofr centerOfView
> select clear
> view sel
> cofr centerOfView
> view sel
> cofr centerOfView
> view sel
> cofr centerOfView
> select clear
> select clear
> view sel
> cofr centerOfView
> select clear
> view sel
> cofr centerOfView
Not saving entity_poly_seq for non-authoritative sequences
> toolshed show "Model Panel"
> close #1.3
> open
/nfs4/suffolk/WorkComplexIC/anaa2/20190412w1118DmcomplexI/model_building/working/1_Isolde_chains_working/I/chainI_working1.pdb
chainI_working1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) NDUFS8 [more info...]
Chain information for chainI_working1.pdb #2
---
Chain | Description
I | No description available
Non-standard residues in chainI_working1.pdb #2
---
SF4 — (SF4)
chainI_working1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) NDUFS8 [more info...]
Chain information for chainI_working1.pdb
---
Chain | Description
2.3/I | No description available
Non-standard residues in chainI_working1.pdb #2.3
---
SF4 — (SF4)
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1289, in _box_moved_cb
self._update_box()
File "/home/anaa2/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 1302, in _update_box
atoms = self.structure.atoms
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
Error processing trigger "spotlight moved":
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/usr/mbu/software/chimerax/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 418.67
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Change History (3)
comment:1 by , 6 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → "spotlight moved" trigger handler using dead Structure |
follow-up: 2 comment:2 by , 6 years ago
Yes, I see what’s happened here. Clipper makes the atomic model subordinate to a higher level “manager” model that handles a lot of the choreography. Wasn’t really designed to be useful beyond the lifetime of the model itself... will have to decide how best to handle things when someone goes and specifically closes the atomic model. Just auto-close the top-level model? Or re-jig things so the model can be safely swapped out for a new one? Will consider.
comment:3 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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I'm guessing that the missing Structure attribute is '_c_pointer', i.e. the Structure is dead.