Close PAE plot with structure

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.4.dev202203290305 (2022-03-29 03:05:53 UTC)
Description
PAE plot should probably close when its associated model is closed.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.4.dev202203290305 (2022-03-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> alphafold fetch P02751 pae true

Fetching compressed AlphaFold P02751 from
https://alphafold.ebi.ac.uk/files/AF-P02751-F1-model_v2.cif  
Chain information for AlphaFold P02751 #1  
---  
Chain | Description | UniProt  
A | Fibronectin | FINC_HUMAN  
  
Fetching compressed AlphaFold PAE P02751 from
https://alphafold.ebi.ac.uk/files/AF-P02751-F1-predicted_aligned_error_v2.json  

> help help:user/tools/alphafold.html

> select /A:550

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add /A:179

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select up

97 atoms, 99 bonds, 12 residues, 1 model selected  

> select add /A:1433

109 atoms, 111 bonds, 13 residues, 1 model selected  

> select add /A:218

118 atoms, 119 bonds, 14 residues, 1 model selected  

> select up

222 atoms, 224 bonds, 29 residues, 1 model selected  

> show sel

> color sel byhetero

> select add /A:184

231 atoms, 232 bonds, 30 residues, 1 model selected  

> select up

244 atoms, 246 bonds, 32 residues, 1 model selected  

> show sel

> \~cartoon sel

Unknown command: \~cartoon sel  

> ~cartoon sel

> cartoon

> hide

> select clear

> close

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 428, in mouseReleaseEvent  
self._rectangle_select_callback(self._down_xy, self._scene_position(event))  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 358, in _rectangle_select  
self._color_residues(min(r1,r3), max(r2,r4), 'lime', 'gray')  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 370, in _color_residues  
all_res = m.residues  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\atomic\molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.6
Locale: en_GB.cp1252
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: windows

Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB

Installed Packages:
    -himerax-isolde: 1.4.dev0
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
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    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
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    ChimeraX-Arrays: 1.0
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    ChimeraX-BasicActions: 1.1
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    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
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    ChimeraX-Dssp: 2.0
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    ChimeraX-ExperimentalCommands: 1.0
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
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    ChimeraX-Hbonds: 2.1.2
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
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[Tom Goddard]

Yep. Will fix this. On vacation today and Friday and meetings Thursday, so probably next week.

[Tom Goddard]

Done.