Opened 15 months ago

Closed 15 months ago

#15668 closed defect (fixed)

Foldseek excludes residues missing backbone N, e.g. PDB 7w7g /B:654

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202407240247 (2024-07-24 02:47:28 UTC)
Description
Foldseek sequence mismatch again.  This time 7w7g chain B which has two leucines :364,654 with no residues between them.  For some reason the foldseek 8jnb results have only one leucine.  Both residues appear unmodified.  Oops, no 654 is missing its N atom.  I guess Foldseek needs the N atom.  Maybe it needs all the backbone atoms.


Log:
UCSF ChimeraX version: 1.9.dev202407240247 (2024-07-24)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Downloads/ChimeraX/Foldseek/8jnb_B/pdb100.m8 format
> foldseek

Summary of feedback from opening
/Users/goddard/Downloads/ChimeraX/Foldseek/8jnb_B/pdb100.m8  
---  
notes | 8jnb.cif title:  
CRAF ras-binding domain chimera, ligand complex [more info...]  
  
  
  
  
| Chain information for 8jnb.cif #1  
  
---  
  
  
Chain  
| Description  
| UniProt  
  
  
  
  
  
B  
| RAF proto-oncogene serine/threonine-protein kinase, CRaf  
| RAF1_HUMAN 50-101 114-141, BRAF_HUMAN 102-113  
  
  
  
  
  
  
  
Non-standard residues in 8jnb.cif #1  
  
---  
  
  
  
  
USX — 2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-
phenoxy]ethanamide  
  
  
  
  
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Foldseek search for similar structures to /B in pdb100 found 845 hits  
  

> foldseek open 7w7g_B

> open 7w7g

7w7g title:  
Structure of Mammalian NALCN-FAM155A-UNC79-UNC80 quanternary complex [more
info...]  
  
Chain information for 7w7g #2  
---  
Chain | Description | UniProt  
A | Protein unc-79 homolog | E5CYJ9_MOUSE 1-2654  
B | Protein unc-80 homolog | B8XCJ6_MOUSE 1-3326  
C | Sodium leak channel non-selective protein | NALCN_RAT 1-1738  
D | Transmembrane protein FAM155A | F155A_MOUSE 1-467  
  
Non-standard residues in 7w7g #2  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
ZN — zinc ion  
  

Foldseek result pdb100 7w7g chain B number of residues 1711 does not match
residues in structure 1710, sequences
PIQTFLWRQTSAFLRPKLGKQYEASCVSFERVLVENKLHGLSPALSEAIQSISRWELVQAALPHVLHCTATLLSNRNKLGHQDKLGVAETKLLHTLHWMLLENSMATVELFVFLFAPLVHRIKESDLTFRLASGLVIWQPMWEYFDVAVLRCLLQPHWSEEGTQWSLMYYLQRLRHMLLSVVLKAVYLVLNHDISSRICDVALNIVECLLQLGVVPCVEPVSNHRLALTMLIKIVKSLQVFRENAQNCLTKLYKLDKIQFRQTMRDYVNKDSLNNVVDFLHALLGFCMEPNVEGIIVGAMFKSLITRCASTTHELHSPENLGLYCDIRQLVQFIKEAHGNVFRRVALSALLDSANLGRKDFWRKMFKSNVVNLGAIRQGMKRFQFLLNCCEPGTIPDASILAAALDLEAPVVARAALFLECARFVHRCNRGNWPEWMKKRNQKLQWSAAKLFYQWGDAIGIRLNELCHETKRRLRKEDEEEDFLDDSTVNPPFALKMAACQLLLEITTFLRETFSCENYHRNMSWLHVMILLCNQQSFICTHVDYCHPHCYLHHSRSCARLVRAIKLLYSGMLKYIRFQVMSLSPAPLSLLIKAAPILTEEMYGDIQPAAWELLLSMDEHMAGAAAAMFLLCAVKVPDAVSDMLMSEFHHAETVQRLNAVLKFHTLWRFRYQVWPRMEEGAQQIFKIPPPSINFTLPSPVLGMPSVPMFDPPWVPQLKNLQQEEEKKRLGREASLITAIPITQEACYEPQAVFPACICAAVLPIVHLMEDGEVREDGVAVSAVAQQVLWNCLIEDPSTVLRHFLEKLTISNRQDELMYMLRKLLLNIGDFPAQTSHILFNYLVGLIMYFVRTPCEWGMDAISATLTFLWEVVGYVEGLFFKDLKQTMKKEQCEVKLLVTASMPGTKTLVVHGQNECDIPTQLPVHEDTQFEALLKECLEFFNIPESQSTHYFLMDKRWNLIHYNKTYVRDIYPFRRSVSPQLNLVHMHPEKGQELIQKQVFTRKLEEVGRVLFLISLTQKIPTAHKQSHVSMLQEDLLRLPSFPRSAIDAEFSLFSDPQAGKELFGLDTLQKSLWIQLLEEMFLGMPSEFPWGDEIMLFLNVFNGALILHPEDSALLRQYAATVINTAVHFNHLFSLSGYQWILPTMLQVYSDYESNPQLRRAIEFACHQFYILHRKPFVLQLFASVAPLLEFKGVSAQCLFDLLQSLEGETTDILDILELVKAEKPLKSLDFCYGNEDLTFSISEAIKLCVTVVAYAPESFRSLQMLMVLEALVPCYLQKMKRQTSQVETVPAAREEIAATAALATSLQALLYSVEVLTRPMTAPEELDERISREEFRRPRESLLNICTEFYKHCGPRLKILQNLAGEPRVTALELLDVKSHMRLAEIAHSLLKLAPYDTQTMESRGLRRYIMEMLPITDWSAEAVRPALILILKRLDRMFNKIHKMPTLRRQVEWEPASSLIEGVCLTLQRQPIISFLPHLRSLINVCVNLVMGVVGPYLSPPLPFSTAVVRLVALQIQALKEDFPLSHVISPFTNQERREGMLLNLLIPFVLTVGSGSKDSPWLEQPEVQLLLQTVINVLLPLAESTSQAAYLALKVILVCFERQLGSQWYWLSLQVKEMALRKVGGLALWDFLDFIVRTRIPIFVLLRPFIQCKLLAQPAENHEELSARQHISDQLERRFIPRPLCKSSLIAEFNSELKILKEAVHS
and
PIQTFLWRQTSAFLRPKLGKQYEASCVSFERVLVENKLHGLSPALSEAIQSISRWELVQAALPHVLHCTATLLSNRNKLGHQDKLGVAETKLLHTLHWMLLENSMATVELFVFLFAPLVHRIKESDLTFRLASGLVIWQPMWEYFDVAVLRCLLQPHWSEEGTQWSLMYYLQRLRHMLSVVLKAVYLVLNHDISSRICDVALNIVECLLQLGVVPCVEPVSNHRLALTMLIKIVKSLQVFRENAQNCLTKLYKLDKIQFRQTMRDYVNKDSLNNVVDFLHALLGFCMEPNVEGIIVGAMFKSLITRCASTTHELHSPENLGLYCDIRQLVQFIKEAHGNVFRRVALSALLDSANLGRKDFWRKMFKSNVVNLGAIRQGMKRFQFLLNCCEPGTIPDASILAAALDLEAPVVARAALFLECARFVHRCNRGNWPEWMKKRNQKLQWSAAKLFYQWGDAIGIRLNELCHETKRRLRKEDEEEDFLDDSTVNPPFALKMAACQLLLEITTFLRETFSCENYHRNMSWLHVMILLCNQQSFICTHVDYCHPHCYLHHSRSCARLVRAIKLLYSGMLKYIRFQVMSLSPAPLSLLIKAAPILTEEMYGDIQPAAWELLLSMDEHMAGAAAAMFLLCAVKVPDAVSDMLMSEFHHAETVQRLNAVLKFHTLWRFRYQVWPRMEEGAQQIFKIPPPSINFTLPSPVLGMPSVPMFDPPWVPQLKNLQQEEEKKRLGREASLITAIPITQEACYEPQAVFPACICAAVLPIVHLMEDGEVREDGVAVSAVAQQVLWNCLIEDPSTVLRHFLEKLTISNRQDELMYMLRKLLLNIGDFPAQTSHILFNYLVGLIMYFVRTPCEWGMDAISATLTFLWEVVGYVEGLFFKDLKQTMKKEQCEVKLLVTASMPGTKTLVVHGQNECDIPTQLPVHEDTQFEALLKECLEFFNIPESQSTHYFLMDKRWNLIHYNKTYVRDIYPFRRSVSPQLNLVHMHPEKGQELIQKQVFTRKLEEVGRVLFLISLTQKIPTAHKQSHVSMLQEDLLRLPSFPRSAIDAEFSLFSDPQAGKELFGLDTLQKSLWIQLLEEMFLGMPSEFPWGDEIMLFLNVFNGALILHPEDSALLRQYAATVINTAVHFNHLFSLSGYQWILPTMLQVYSDYESNPQLRRAIEFACHQFYILHRKPFVLQLFASVAPLLEFKGVSAQCLFDLLQSLEGETTDILDILELVKAEKPLKSLDFCYGNEDLTFSISEAIKLCVTVVAYAPESFRSLQMLMVLEALVPCYLQKMKRQTSQVETVPAAREEIAATAALATSLQALLYSVEVLTRPMTAPEELDERISREEFRRPRESLLNICTEFYKHCGPRLKILQNLAGEPRVTALELLDVKSHMRLAEIAHSLLKLAPYDTQTMESRGLRRYIMEMLPITDWSAEAVRPALILILKRLDRMFNKIHKMPTLRRQVEWEPASSLIEGVCLTLQRQPIISFLPHLRSLINVCVNLVMGVVGPYLSPPLPFSTAVVRLVALQIQALKEDFPLSHVISPFTNQERREGMLLNLLIPFVLTVGSGSKDSPWLEQPEVQLLLQTVINVLLPLAESTSQAAYLALKVILVCFERQLGSQWYWLSLQVKEMALRKVGGLALWDFLDFIVRTRIPIFVLLRPFIQCKLLAQPAENHEELSARQHISDQLERRFIPRPLCKSSLIAEFNSELKILKEAVHS.  

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/foldseek.py", line 871, in foldseek_open  
open_hit(session, hit, query_chain, trim = trim,  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/foldseek.py", line 410, in open_hit  
aligned_res = trim_structure(structure, hit, trim, log = log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/foldseek.py", line 464, in trim_structure  
rnum_start, rnum_end = res[0].number, res[-1].number  
~~~^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/foldseek.py", line 464, in trim_structure  
rnum_start, rnum_end = res[0].number, res[-1].number  
~~~^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/B

Alignment identifier is 2/B  

> select
> #2/B:22-35,41-53,62-100,106-122,181-193,206-220,331-340,345-364,655-666,670-685,787-803,825-856,860-874,899-924,927-959,1026-1038,1177-1195,1202-1209,1215-1235,1266-1294,1312-1321,1340-1358,1528-1538,1553-1572,1625-1634,1639-1670,1672-1703,1706-1732,1804-1820,1826-1831,1912-1926,1937-1968,1970-1986,1989-2010,2014-2031,2037-2055,2087-2099,2125-2130,2146-2179,2183-2198,2200-2207,2209-2214,2219-2242,2252-2268,2271-2294,2297-2312,2315-2346,2364-2377,2385-2389,2410-2425,2428-2482,2547-2585,2598-2616,2619-2635,2646-2666,2669-2714,2738-2756,2761-2770,2774-2792,2801-2817,2855-2878,2880-2895,2900-2926,2934-2949,2959-2979

10435 atoms, 10586 bonds, 1286 residues, 1 model selected  

> select clear

> select #2/B:LYS

698 atoms, 622 bonds, 1 pseudobond, 78 residues, 2 models selected  

> select #2/B:LEU

2047 atoms, 1827 bonds, 1 pseudobond, 256 residues, 2 models selected  

> select clear

> select #2/B:LEU

2047 atoms, 1827 bonds, 1 pseudobond, 256 residues, 2 models selected  

> select #2/B:654

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/B:654-655

13 atoms, 12 bonds, 2 residues, 1 model selected  

> view sel

> select #2/B:364

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/B:364

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view sel

> select #2/B:364-654

15 atoms, 13 bonds, 1 pseudobond, 2 residues, 2 models selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel atoms

> view sel

> hide sel cartoons

> select clear

> hide cartoons




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 36 days, 20 hours, 12 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    biopython: 1.83
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.6
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.3
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.5
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.3
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.0
    ChimeraX-clix: 0.1.4
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9.dev202407240247
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-Foldseek: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
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    ChimeraX-IHM: 1.1
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    ChimeraX-IO: 1.0.1
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    ChimeraX-Map: 1.2
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    ChimeraX-MapEraser: 1.0.1
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    ChimeraX-MapFit: 2.0
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    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
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    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NIHPresets: 1.1.19
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    ChimeraX-NRRD: 1.1
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    ChimeraX-OpenCommand: 1.13.4
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    ChimeraX-PDB: 2.7.5
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    ChimeraX-Positions: 1.0
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    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
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    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-Segger: 1.0
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    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.8
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    fsspec: 2024.3.1
    funcparserlib: 2.0.0a0
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    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
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    jedi: 0.19.1
    Jinja2: 3.1.3
    joblib: 1.4.2
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    llvmlite: 0.42.0
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    mpmath: 1.3.0
    mrcfile: 1.5.0
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
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Change History (6)

comment:1 by Tom Goddard, 15 months ago

Component: Unassigned → Structure Analysis
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Foldseek excludes residues missing backbone N, e.g. PDB 7w7g /B:654

comment:2 by Tom Goddard, 15 months ago

PDB 3u8z /C:20 is also missing its N atom.

comment:3 by Tom Goddard, 15 months ago

The problem is not that Foldseek requires an N atom. It does not. The problem was in the opposite direction, that ChimeraX excluded a residue because residue.principal_atom was None even though it had a CA atom if the N atom is missing. That seems bad. But I see the C++ code is not looking at Residue::polymer_type() so it is trying to guess whether the residue is an amino acid by looking for the N and C backbone atoms. I've asked Eric if this can be fixed.

comment:4 by Tom Goddard, 15 months ago

Using the CA atoms instead of principal_atom fixed the 5 sequence mismatch cases among the 845 hits for query 8jnb.

Many other places in the ChimeraX foldseek code are using principal_atom, especially for the query sequence to get the CA atom, and those will have to be changed if the principal_atom code cannot be fixed.

comment:6 by Tom Goddard, 15 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

I made ChimeraX foldseek code use Residues.find_existing_atoms("CA") instead of Residues.existing_principal_atoms. It is clearer what the code is doing by explicitly asking for the CA atoms, and it always works.

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