Alphafold match: 'Structure' object has no attribute 'num_observed_residues'

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202110222254 (2021-10-22 22:54:52 UTC)
Description
open 7cfd
alphafold match #1

MatchMaker throws an error on chain O (which has a UniProt ID but only a single residue modelled), and the session ends up pretty borked - atoms from the AF models appear to be added to the session, but don't appear in the Models panel and are drawn as featureless white spheres.


Log:
UCSF ChimeraX version: 1.3rc202110222254 (2021-10-22)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7cfd structureFactors true

Summary of feedback from opening 7cfd fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 7cfd from
http://files.rcsb.org/download/7cfd.cif  
Fetching CCD 2MR from http://ligand-expo.rcsb.org/reports/2/2MR/2MR.cif  
Fetching compressed 7cfd structure factors from
http://files.rcsb.org/download/7cfd-sf.cif  
Resolution: 2.703675434227976  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 30,32,28, pixel
0.899,0.845,0.886, shown at level 0.258, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 30,32,28, pixel
0.899,0.845,0.886, shown at level -0.121,0.121, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_18 as #1.1.1.4, grid size 30,32,28, pixel
0.899,0.845,0.886, shown at level 0.473, step 1, values float32  
7cfd title:  
Drosophila melanogaster Krimper eTud2-AubR15me2 complex [more info...]  
  
Chain information for 7cfd  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H | FI20010p1 | A1ZAC4_DROME  
1.2/I 1.2/J 1.2/K 1.2/L 1.2/M 1.2/N 1.2/O 1.2/Z | Protein aubergine |
AUB_DROME  
  
7cfd mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
5| author_defined_assembly  
6| author_defined_assembly  
7| author_defined_assembly  
8| author_defined_assembly  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 106 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 30,32,28, pixel
0.899,0.845,0.886, shown at level 0.276, step 1, values float32  
Done loading forcefield  

> alphafold match #1

Fetching compressed AlphaFold A1ZAC4 from
https://alphafold.ebi.ac.uk/files/AF-A1ZAC4-F1-model_v1.cif  
Fetching compressed AlphaFold O76922 from
https://alphafold.ebi.ac.uk/files/AF-O76922-F1-model_v1.cif  
Fewer than 3 residues aligned; cannot match 7cfd, chain O with AlphaFold
O76922, chain O  
2 AlphaFold models found using UniProt identifiers: A1ZAC4 (chains
B,C,D,E,F,A,G,H), O76922 (chains I,J,K,L,N,M,Z,O)  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 53, in alphafold_match  
session.models.add(mlist)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 676, in add  
m.added_to_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 405, in <lambda>  
group.added_to_session = lambda session, g=group: _log_alphafold_chain_info(g)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 418, in _log_alphafold_chain_info  
_log_alphafold_chain_table(am.child_models(), struct_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\alphafold\match.py", line 438, in _log_alphafold_chain_table  
m.num_residues, m.num_observed_residues, pct_id))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'num_observed_residues'  
  
AttributeError: 'Structure' object has no attribute 'num_observed_residues'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> select #1/O

13 atoms, 12 bonds, 1 residue, 1 model selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #1

> show #1

> hide #2

> show #2




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
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
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    -himerax-clipper: 0.17.0
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
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    ChimeraX-BuildStructure: 2.6
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    ChimeraX-ChemGroup: 2.0
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    ChimeraX-ColorActions: 1.0
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    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202110222254
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev33
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
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    ChimeraX-Maestro: 1.8.1
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    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
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    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
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    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
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    ChimeraX-ReadPbonds: 1.0
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    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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
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    ChimeraX-ShowAttr: 1.0
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    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
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[Tom Goddard]

Fixed in 1.3 and 1.4.

When alignment of alphafold model to an experimental structure chain fails because the experimental structure chain has fewer than 3 residues the code was not setting the alphafold model attribute that said how many experimental residues were present. Made it set the attribute even if alignment fails.

Thanks for reporting the problem.