Bad AlphaFold model trimming

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3.dev202107240347 (2021-07-24 03:47:26 UTC)
Description
Something going wrong with the model trimming when fetching the AlphaFold prediction for 7ck3 - the trimmed model contains almost nothing (quite a bit of it wrong), while the untrimmed version shows most of the structure is correctly predicted with high confidence.

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> 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}
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color bychain; color byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3.dev202107240347 (2021-07-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7o4f

7o4f title:  
The DYW domain of A. thaliana OTP86 in its active state [more info...]  
  
Chain information for 7o4f #1  
---  
Chain | Description | UniProt  
A B D G | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
| PP296_ARATH  
  
Non-standard residues in 7o4f #1  
---  
ZN — zinc ion  
  
7o4f mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> open #1 fromDatabase AlphaFold

Summary of feedback from opening #1 fetched from AlphaFold  
---  
notes | Fetching compressed AlphaFold Q9M1V3 from
https://alphafold.ebi.ac.uk/files/AF-Q9M1V3-F1-model_v1.cif  
7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2  
Matchmaker 7o4f, chain A (#1) with AlphaFold Q9M1V3, chain A (#), sequence
alignment score = 654.4  
RMSD between 102 pruned atom pairs is 0.619 angstroms; (across all 135 pairs:
4.767)  
  
7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2  
Matchmaker 7o4f, chain B (#1) with AlphaFold Q9M1V3, chain B (#), sequence
alignment score = 646.3  
RMSD between 103 pruned atom pairs is 0.590 angstroms; (across all 135 pairs:
4.891)  
  
7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2  
Matchmaker 7o4f, chain D (#1) with AlphaFold Q9M1V3, chain D (#), sequence
alignment score = 654.4  
RMSD between 103 pruned atom pairs is 0.611 angstroms; (across all 135 pairs:
4.759)  
  
7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2  
Matchmaker 7o4f, chain G (#1) with AlphaFold Q9M1V3, chain G (#), sequence
alignment score = 647.2  
RMSD between 103 pruned atom pairs is 0.592 angstroms; (across all 135 pairs:
4.901)  
  
Chain information for UniProt Q9M1V3 chain A #2.1  
---  
Chain | Description | UniProt  
A | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic |
PP296_ARATH  
  
Chain information for UniProt Q9M1V3 chain B #2.2  
---  
Chain | Description  
B | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic  
  
Chain information for UniProt Q9M1V3 chain D #2.3  
---  
Chain | Description  
D | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic  
  
Chain information for UniProt Q9M1V3 chain G #2.4  
---  
Chain | Description  
G | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic  
  
Opened 4 AlphaFold chain models  

> ui tool show Shell

> save 7o4f.pdb #1

Fetching compressed Alphafold Q9M1V3 PAE from
https://alphafold.ebi.ac.uk/files/AF-Q9M1V3-F1-predicted_aligned_error_v1.json  

> color byattribute r:isolde_domain #2.4 target ra palette rainbow

[Repeated 1 time(s)]1101 atoms, 135 residues, atom isolde_domain range -1 to 4  

> hide #2.1 models

> hide #2.2 models

> hide #2.3 models

> color byattribute r:isolde_domain #2.4 target ra palette rainbow

1101 atoms, 135 residues, atom isolde_domain range -1 to 13  

> color byattribute r:isolde_domain #2.4 target ra palette rainbow

1101 atoms, 135 residues, atom isolde_domain range -1 to 23  

> color byattribute r:isolde_domain #2.4 target ra palette rainbow

1101 atoms, 135 residues, atom isolde_domain range -1 to 0  

> color byattribute r:isolde_domain #2.4 target ra palette rainbow

1101 atoms, 135 residues, atom isolde_domain range -1 to 87  

> close #1-2

> open 7cfd

7cfd title:  
Drosophila melanogaster Krimper eTud2-AubR15me2 complex [more info...]  
  
Chain information for 7cfd #1  
---  
Chain | Description | UniProt  
A B C D E F G H | FI20010p1 | A1ZAC4_DROME  
I J K L M N O 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  
  

> cartoon

> hide

> open #1 fromDatabase AlphaFold

Summary of feedback from opening #1 fetched from AlphaFold  
---  
error | Fewer than 3 residues aligned; cannot match 7cfd, chain O with
AlphaFold O76922, chain O  
notes | 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8  
Matchmaker 7cfd, chain B (#1) with AlphaFold A1ZAC4, chain B (#), sequence
alignment score = 929  
RMSD between 125 pruned atom pairs is 0.984 angstroms; (across all 178 pairs:
2.118)  
  
Fetching compressed AlphaFold O76922 from
https://alphafold.ebi.ac.uk/files/AF-O76922-F1-model_v1.cif  
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8  
Matchmaker 7cfd, chain I (#1) with AlphaFold O76922, chain I (#), sequence
alignment score = 48.2  
RMSD between 4 pruned atom pairs is 0.867 angstroms; (across all 4 pairs:
0.867)  
  
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8  
Matchmaker 7cfd, chain C (#1) with AlphaFold A1ZAC4, chain C (#), sequence
alignment score = 935  
RMSD between 141 pruned atom pairs is 1.018 angstroms; (across all 179 pairs:
1.674)  
  
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8  
Matchmaker 7cfd, chain J (#1) with AlphaFold O76922, chain J (#), sequence
alignment score = 51.8  
RMSD between 6 pruned atom pairs is 1.261 angstroms; (across all 7 pairs:
1.648)  
  
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8  
Matchmaker 7cfd, chain K (#1) with AlphaFold O76922, chain K (#), sequence
alignment score = 53  
RMSD between 8 pruned atom pairs is 1.551 angstroms; (across all 8 pairs:
1.551)  
  
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8  
Matchmaker 7cfd, chain D (#1) with AlphaFold A1ZAC4, chain D (#), sequence
alignment score = 925.4  
RMSD between 136 pruned atom pairs is 0.934 angstroms; (across all 178 pairs:
1.734)  
  
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8  
Matchmaker 7cfd, chain E (#1) with AlphaFold A1ZAC4, chain E (#), sequence
alignment score = 905.6  
RMSD between 155 pruned atom pairs is 1.177 angstroms; (across all 180 pairs:
1.888)  
  
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8  
Matchmaker 7cfd, chain L (#1) with AlphaFold O76922, chain L (#), sequence
alignment score = 48.2  
RMSD between 4 pruned atom pairs is 1.100 angstroms; (across all 4 pairs:
1.100)  
  
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8  
Matchmaker 7cfd, chain F (#1) with AlphaFold A1ZAC4, chain F (#), sequence
alignment score = 936.2  
RMSD between 143 pruned atom pairs is 1.059 angstroms; (across all 182 pairs:
1.673)  
  
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8  
Matchmaker 7cfd, chain A (#1) with AlphaFold A1ZAC4, chain A (#), sequence
alignment score = 931.4  
RMSD between 131 pruned atom pairs is 1.015 angstroms; (across all 176 pairs:
1.780)  
  
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8  
Matchmaker 7cfd, chain G (#1) with AlphaFold A1ZAC4, chain G (#), sequence
alignment score = 933.8  
RMSD between 147 pruned atom pairs is 1.263 angstroms; (across all 181 pairs:
1.573)  
  
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8  
Matchmaker 7cfd, chain N (#1) with AlphaFold O76922, chain N (#), sequence
alignment score = 50.6  
RMSD between 5 pruned atom pairs is 1.368 angstroms; (across all 6 pairs:
1.962)  
  
5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8  
Matchmaker 7cfd, chain H (#1) with AlphaFold A1ZAC4, chain H (#), sequence
alignment score = 870.2  
RMSD between 151 pruned atom pairs is 1.283 angstroms; (across all 181 pairs:
1.594)  
  
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8  
Matchmaker 7cfd, chain M (#1) with AlphaFold O76922, chain M (#), sequence
alignment score = 50.6  
RMSD between 5 pruned atom pairs is 0.710 angstroms; (across all 6 pairs:
1.685)  
  
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8  
Matchmaker 7cfd, chain Z (#1) with AlphaFold O76922, chain Z (#), sequence
alignment score = 47  
RMSD between 3 pruned atom pairs is 0.729 angstroms; (across all 3 pairs:
0.729)  
  
6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8  
Matchmaker 7cfd, chain O (#1) with AlphaFold O76922, chain O (#), sequence
alignment score = 44.6  
  
Chain information for UniProt A1ZAC4 chain B #2.1  
---  
Chain | Description  
B | FI20010p1  
  
Chain information for UniProt O76922 chain I #2.2  
---  
Chain | Description  
I | Protein aubergine  
  
Chain information for UniProt A1ZAC4 chain C #2.3  
---  
Chain | Description  
C | FI20010p1  
  
Chain information for UniProt O76922 chain J #2.4  
---  
Chain | Description  
J | Protein aubergine  
  
Chain information for UniProt O76922 chain K #2.5  
---  
Chain | Description  
K | Protein aubergine  
  
Chain information for UniProt A1ZAC4 chain D #2.6  
---  
Chain | Description  
D | FI20010p1  
  
Chain information for UniProt A1ZAC4 chain E #2.7  
---  
Chain | Description  
E | FI20010p1  
  
Chain information for UniProt O76922 chain L #2.8  
---  
Chain | Description  
L | Protein aubergine  
  
Chain information for UniProt A1ZAC4 chain F #2.9  
---  
Chain | Description  
F | FI20010p1  
  
Chain information for UniProt A1ZAC4 chain A #2.10  
---  
Chain | Description | UniProt  
A | FI20010p1 | A1ZAC4_DROME  
  
Chain information for UniProt A1ZAC4 chain G #2.11  
---  
Chain | Description  
G | FI20010p1  
  
Chain information for UniProt O76922 chain N #2.12  
---  
Chain | Description  
N | Protein aubergine  
  
Chain information for UniProt A1ZAC4 chain H #2.13  
---  
Chain | Description  
H | FI20010p1  
  
Chain information for UniProt O76922 chain M #2.14  
---  
Chain | Description  
M | Protein aubergine  
  
Chain information for UniProt O76922 chain Z #2.15  
---  
Chain | Description  
Z | Protein aubergine  
  
Chain information for UniProt O76922 chain O #2.16  
---  
Chain | Description  
O | Protein aubergine  
  
Opened 16 AlphaFold chain models  

> hide #2.16 models

> show #2.16 models

> select #2.1

1521 atoms, 1562 bonds, 185 residues, 1 model selected  
Fetching compressed Alphafold A1ZAC4 PAE from
https://alphafold.ebi.ac.uk/files/AF-A1ZAC4-F1-predicted_aligned_error_v1.json  

> color byattribute r:isolde_domain #2.1 target ra palette rainbow

1521 atoms, 185 residues, atom isolde_domain range -1 to 110  

> color byattribute r:isolde_domain #2.1 target ra palette rainbow

1521 atoms, 185 residues, atom isolde_domain range -1 to 9  

> hide ~sel models

> show #!2 models

> select clear

> color byattribute r:isolde_domain #2.1 target ra palette rainbow

1521 atoms, 185 residues, atom isolde_domain range -1 to 16  

> color byattribute r:isolde_domain #2.1 target ra palette rainbow

1521 atoms, 185 residues, atom isolde_domain range -1 to 17  

> save 7cfd.pdb #1

> save AF_A1ZAC4_cluster_0.pdb #2.1 selectedOnly true

> save AF_A1ZAC4_cluster_1.pdb #2.1 selectedOnly true

> select clear

> open 7cfb

7cfb title:  
Drosophila melanogaster Krimper eTud1 apo structure [more info...]  
  
Chain information for 7cfb #3  
---  
Chain | Description | UniProt  
A B | FI20010p1 | A1ZAC4_DROME  
  
Non-standard residues in 7cfb #3  
---  
SO4 — sulfate ion  
  
7cfb mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7cfd, chain H (#1) with 7cfb, chain B (#3), sequence alignment
score = 114.8  
RMSD between 83 pruned atom pairs is 1.228 angstroms; (across all 143 pairs:
5.190)  
  

> matchmaker #3 to #2.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker UniProt A1ZAC4 chain B, chain B (#2.1) with 7cfb, chain B (#3),
sequence alignment score = 99.8  
RMSD between 76 pruned atom pairs is 1.068 angstroms; (across all 143 pairs:
5.602)  
  

> save 7cfb.pdb #3

> close #1-2#3

> open 7ciw

7ciw title:  
Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with
Ac-Agm and CoA [more info...]  
  
Chain information for 7ciw #1  
---  
Chain | Description | UniProt  
A | Agmatine N-acetyltransferase | Q9W469_DROME  
  
Non-standard residues in 7ciw #1  
---  
COA — coenzyme A  
G0R — N-(4-carbamimidamidobutyl)ethanamide  
  

> open #1 fromDatabase AlphaFold

Summary of feedback from opening #1 fetched from AlphaFold  
---  
notes | Fetching compressed AlphaFold Q9W469 from
https://alphafold.ebi.ac.uk/files/AF-Q9W469-F1-model_v1.cif  
1673 atoms, 216 residues, atom bfactor range 40.4 to 98.9  
Matchmaker 7ciw, chain A (#1) with AlphaFold Q9W469, chain A (#), sequence
alignment score = 1100.6  
RMSD between 208 pruned atom pairs is 0.547 angstroms; (across all 216 pairs:
3.620)  
  
Chain information for UniProt Q9W469 chain A  
---  
Chain | Description | UniProt  
2.1/A | Agmatine N-acetyltransferase | Q9W469_DROME  
  
Opened 1 AlphaFold chain models  

> close #1#2

> open 7ck3

7ck3 title:  
Crystal structure of Arabidopsis CESA3 catalytic domain [more info...]  
  
Chain information for 7ck3 #1  
---  
Chain | Description | UniProt  
A B | Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose
synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH  
  
7ck3 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> open #1 fromDatabase AlphaFold

Summary of feedback from opening #1 fetched from AlphaFold  
---  
notes | 8430 atoms, 1065 residues, atom bfactor range 23 to 97.8  
Matchmaker 7ck3, chain A (#1) with AlphaFold Q941L0, chain A (#), sequence
alignment score = 1592  
RMSD between 50 pruned atom pairs is 0.916 angstroms; (across all 98 pairs:
9.484)  
  
8430 atoms, 1065 residues, atom bfactor range 23 to 97.8  
Matchmaker 7ck3, chain B (#1) with AlphaFold Q941L0, chain B (#), sequence
alignment score = 1598.3  
RMSD between 51 pruned atom pairs is 0.926 angstroms; (across all 98 pairs:
9.558)  
  
Chain information for UniProt Q941L0 chain A #2.1  
---  
Chain | Description | UniProt  
A | Cellulose synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH  
  
Chain information for UniProt Q941L0 chain B #2.2  
---  
Chain | Description  
B | Cellulose synthase A catalytic subunit 3 [UDP-forming]  
  
Opened 2 AlphaFold chain models  

> open #1 fromDatabase AlphaFold trim false

Summary of feedback from opening #1 fetched from AlphaFold  
---  
notes | 8430 atoms, 1065 residues, atom bfactor range 23 to 97.8  
Matchmaker 7ck3, chain A (#1) with AlphaFold Q941L0, chain A (#), sequence
alignment score = 1890.2  
RMSD between 268 pruned atom pairs is 0.836 angstroms; (across all 369 pairs:
5.904)  
  
8430 atoms, 1065 residues, atom bfactor range 23 to 97.8  
Matchmaker 7ck3, chain B (#1) with AlphaFold Q941L0, chain B (#), sequence
alignment score = 1903.7  
RMSD between 270 pruned atom pairs is 0.856 angstroms; (across all 369 pairs:
5.907)  
  
Chain information for UniProt Q941L0 chain A #3.1  
---  
Chain | Description | UniProt  
A | Cellulose synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH  
  
Chain information for UniProt Q941L0 chain B #3.2  
---  
Chain | Description  
B | Cellulose synthase A catalytic subunit 3 [UDP-forming]  
  
Opened 2 AlphaFold chain models  

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #2

> hide #2

> show #!3 models

> color bfactor #3

16860 atoms, 2130 residues, atom bfactor range 23 to 97.8  

> select #3&@@bfactor>50

13038 atoms, 13380 bonds, 1632 residues, 2 models selected  

> select #3&@@bfactor>70

12158 atoms, 12492 bonds, 1518 residues, 2 models selected  

> select clear

> hide #!3 models

> show #!3 models

> hide #!2 models




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         13G         35G        306M         13G         48G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', '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: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
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    ChimeraX-AtomicLibrary: 4.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    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: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202107240347
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev32
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    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
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.4
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.6.2
    ChimeraX-PDB: 2.4.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    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-Sample: 0.1
    ChimeraX-SaveCommand: 1.4.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.10.1
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-Voyager: 0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.3.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    numpydoc: 1.1.0
    OpenMM: 7.6.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    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: 22.1.0
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.0.post1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    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: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

[Tom Goddard]

This was fixed last Tuesday (July 27). Fix is is current daily builds. I am improving alphafold fetch every day, so best to use the most recent version.

[Tom Goddard]

Oops! Added the previous comment to the wrong ticket. This problem still is present and likely has to do with a residue numbering issue and I will be looking at it today.

[Tom Goddard]

PDB entry 7ck3 lists two subsequences of the Uniprot sequence for each chain. I never saw this before, only saw one sequence interval listed. Trimming code will need to be adapted to handle multiple sequence ranges.

From 7ck3.cif:

loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_db_align_beg_ins_code
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_db_align_end_ins_code
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 7CK3 A 1 ? 314 ? Q941L0 317 ? 630 ? 317 630
2 2 7CK3 A 320 ? 429 ? Q941L0 702 ? 811 ? 702 811
3 1 7CK3 B 1 ? 314 ? Q941L0 317 ? 630 ? 317 630
4 2 7CK3 B 320 ? 429 ? Q941L0 702 ? 811 ? 702 811

[Tristan Croll]

Don't want to keep spamming you with new tickets (also buried in preparing for a talk tomorrow), but "open 6w1s; open #1 from alphafold" causes a traceback in my current installation:

Traceback (most recent call last):
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 280, in execute
    cmd.run(cmd_text)
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856, in run
    result = ci.function(session, **kw_args)
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118, in cmd_open
    models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856, in run
    result = ci.function(session, **kw_args)
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 150, in provider_open
    models, status = collated_open(session, database_name, ident,
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 433, in collated_open
    return remember_data_format()
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 404, in remember_data_format
    models, status = func(*func_args, **func_kw)
  File "/home/tic20/.local/share/ChimeraX/1.3/site-packages/chimerax/alphafold/__init__.py", line 26, in fetch
    return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
  File "/home/tic20/.local/share/ChimeraX/1.3/site-packages/chimerax/alphafold/fetch_alphafold.py", line 27, in fetch_alphafold
    return fetch_alphafold_for_chains(session, chains,
  File "/home/tic20/.local/share/ChimeraX/1.3/site-packages/chimerax/alphafold/fetch_alphafold.py", line 86, in fetch_alphafold_for_chains
    _rename_chains(alphafold_model, chain)
  File "/home/tic20/.local/share/ChimeraX/1.3/site-packages/chimerax/alphafold/fetch_alphafold.py", line 161, in _rename_chains
    schains = structure.chains
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/core/attributes.py", line 61, in _getattr_
    return base.__getattr__(self, attr_name, look_in_class=base)
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/core/attributes.py", line 57, in _getattr_
    return look_in_class._attr_registration.get_attr(attr_name)
  File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/core/attributes.py", line 83, 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 'chains' property raised AttributeError

AttributeError: Execution of 'Structure' object's 'chains' property raised AttributeError

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/core/attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised AttributeError" % (self.class_.__name__, attr_name)) from None
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 August 2021 19:44
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4981: Bad AlphaFold model trimming

#4981: Bad AlphaFold model trimming
------------------------------------+-------------------------
          Reporter:  Tristan Croll  |      Owner:  Tom Goddard
              Type:  defect         |     Status:  reopened
          Priority:  normal         |  Milestone:
         Component:  Input/Output   |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------

Comment (by Tom Goddard):

 PDB entry 7ck3 lists two subsequences of the Uniprot sequence for each
 chain.  I never saw this before, only saw one sequence interval listed.
 Trimming code will need to be adapted to handle multiple sequence ranges.

 From 7ck3.cif:

 loop_
 _struct_ref_seq.align_id
 _struct_ref_seq.ref_id
 _struct_ref_seq.pdbx_PDB_id_code
 _struct_ref_seq.pdbx_strand_id
 _struct_ref_seq.seq_align_beg
 _struct_ref_seq.pdbx_seq_align_beg_ins_code
 _struct_ref_seq.seq_align_end
 _struct_ref_seq.pdbx_seq_align_end_ins_code
 _struct_ref_seq.pdbx_db_accession
 _struct_ref_seq.db_align_beg
 _struct_ref_seq.pdbx_db_align_beg_ins_code
 _struct_ref_seq.db_align_end
 _struct_ref_seq.pdbx_db_align_end_ins_code
 _struct_ref_seq.pdbx_auth_seq_align_beg
 _struct_ref_seq.pdbx_auth_seq_align_end
 1 1 7CK3 A 1   ? 314 ? Q941L0 317 ? 630 ? 317 630
 2 2 7CK3 A 320 ? 429 ? Q941L0 702 ? 811 ? 702 811
 3 1 7CK3 B 1   ? 314 ? Q941L0 317 ? 630 ? 317 630
 4 2 7CK3 B 320 ? 429 ? Q941L0 702 ? 811 ? 702 811

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4981#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[goddard@…]

Thanks!  Keep sending the bugs.  You help me make this work well.  I prefer they are in separate tickets but don’t worry about this one - I will make the new ticket for it.

[Tom Goddard]

I made separate ticket #4994 for the traceback in comment 5. I was not able to reproduce that error where somehow structure.chains fails.

[Tom Goddard]

Fixed.

PDB 7ck3 chain A has two separate segments with uniprot ids in the mmCIF file. The fetching code was only handling the one uniprot segment per chain. In this file there are two segments specified in the mmCIF struct_ref_seq table, both with the same uniprot id. I guess this is to handle a deleted interval in the sample sequence. But other structures likely have chimeric sequences where two segments have different uniprot ids. The new code will load each segment for a chain as a separate AlphaFold model. So 7ck3 now loads two AlphaFold models for chain A. The fetch "search true" option gets just one longer segment because the sequence search only produces one longer segment.