Execution of 'Structure' object's '_graphics_changed' property raised AttributeError

[Tom Goddard]

The following command (must be on one line) causes nucleotides to call its _rebuild_molecule('internal', mol) function on apparently a deleted molecule. Due to attribute registration code this produces a pretty cryptic error message (which Eric says he cannot improve), but the real error when I commented out the attribute registration setting of a getattr method was that no attribute c_pointer_ref in mol.

open 4CMP fromDatabase pdb; open 4ZT0 fromDatabase pdb; split #1; split #2; close # 1.2; close #2.3; close #2.4

UCSF ChimeraX version: 0.7 (2018-06-05)
OpenGL version: 4.1 NVIDIA-10.30.25 355.11.10.10.30.120
OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation
How to cite UCSF ChimeraX
open 4CMP fromDatabase pdb
Summary of feedback from opening 4CMP fetched from pdb
notes Used PDBx fixed column width tables to speed up reading mmCIF file
Used PDBx keywords to speed up reading mmCIF file
Chain information for 4cmp #1
Chain Description
A B crispr-associated endonuclease CAS9/CSN1
4cmp mmCIF Assemblies
1 author_and_software_defined_assembly
2 author_and_software_defined_assembly

4cmp citation:
Jinek, M., Jiang, F., Taylor, D.W., Sternberg, S.H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., Kaplan, M., Iavarone, A.T., Charpentier, E., Nogales, E., Doudna, J.A. (2014). Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation. Science, 343, 47997

Opened mmCIF data containing 38285 atoms and 38375 bonds
open 4ZT0 fromDatabase pdb
Summary of feedback from opening 4ZT0 fetched from pdb
notes Used PDBx fixed column width tables to speed up reading mmCIF file
Used PDBx keywords to speed up reading mmCIF file
Chain information for 4zt0 #2
Chain Description
A C CRISPR-associated endonuclease Cas9
B D single-guide RNA
4zt0 mmCIF Assemblies
1 author_and_software_defined_assembly
2 author_and_software_defined_assembly

4zt0 citation:
Jiang, F., Zhou, K., Ma, L., Gressel, S., Doudna, J.A. (2015). A Cas9-guide RNA complex preorganized for target DNA recognition. Science, 348, 1477-1481

Opened mmCIF data containing 23790 atoms and 24530 bonds
split #1
Chain information for 4cmp A #1.1
Chain Description
A No description available
Chain information for 4cmp B #1.2
Chain Description
B No description available
Split 4cmp (#1) into 2 models
split #2
Chain information for 4zt0 A #2.1
Chain Description
A No description available
Chain information for 4zt0 B #2.2
Chain Description
B No description available
Chain information for 4zt0 C #2.3
Chain Description
C No description available
Chain information for 4zt0 D #2.4
Chain Description
D No description available
Split 4zt0 (#2) into 4 models
close # 1.2
close #2.3
close #2.4
Error processing trigger "new frame"
Traceback (most recent call last):
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/triggerset.py", line 126, in invoke
return self._func(self._name, data)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/nucleotides/_data.py", line 487, in rebuild
_rebuild_molecule('internal', mol)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/nucleotides/_data.py", line 606, in _rebuild_molecule
mol.bounds() # need to recompute ribbon first TODO: another way?
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 1591, in bounds
self._update_graphics_if_needed() # Ribbon bound computed from graphics
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 363, in _update_graphics_if_needed
gc = self._graphics_changed
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/attr_registration.py", line 43, in getattr
return base.getattr(self, attr_name, look_in_class=base)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/attr_registration.py", line 39, in getattr
return look_in_class._attr_registration.get_attr(attr_name)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/attr_registration.py", line 64, 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 '_graphics_changed' property raised AttributeError

[Greg Couch]

Doesn't happen in nogui mode. Fixed by added 'if not mol.deleted:'