Opened 3 years ago

Closed 3 years ago

#8566 closed defect (fixed)

AlphaFold/Blast: Needleman-Wunsch being passed structure, not sequence

Reported by: ubaumann@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc: Zach Pearson, Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.dev202302070220 (2023-02-07 02:20:43 UTC)
Description
AlphaFold prediction loading

Log:
UCSF ChimeraX version: 1.6.dev202302070220 (2023-02-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

Populating font family aliases took 1229 ms. Replace uses of missing font
family "Monospace" with one that exists to avoid this cost.  

> alphafold search
> MMRRLLTSLLAALLAVPLLSLSPYPAAHGVLLEESGLDVQTIPSHDVLGRIVIVPETDFSFDEANETIRTLARIDRRILEQAANHHIYIQLLTNPITDEPIARHLRGKTPRGYVPGSKTWDEVPGIGGAHLVLVRLGHSEKGKGHGSINLELHEFAHSLDYIVFDHIHETDEFQALWREEAPQLFPREYYFLTYPEEYFAESFAYYYVSEKTQETLRMAAPRTYTFIRQLAERAS

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Webservices job id: 1O7FZ1UZFHQXD9FW  

> alphafold predict
> MMRRLLTSLLAALLAVPLLSLSPYPAAHGVLLEESGLDVQTIPSHDVLGRIVIVPETDFSFDEANETIRTLARIDRRILEQAANHHIYIQLLTNPITDEPIARHLRGKTPRGYVPGSKTWDEVPGIGGAHLVLVRLGHSEKGKGHGSINLELHEFAHSLDYIVFDHIHETDEFQALWREEAPQLFPREYYFLTYPEEYFAESFAYYYVSEKTQETLRMAAPRTYTFIRQLAERAS

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
[Repeated 2 time(s)]

> alphafold fetch A4INY2 version 4

Fetching compressed AlphaFold A4INY2 from
https://alphafold.ebi.ac.uk/files/AF-A4INY2-F1-model_v4.cif  
Chain information for AlphaFold A4INY2 #1  
---  
Chain | Description | UniProt  
A | Uncharacterized protein | A4INY2_GEOTN 1-235  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 239, in <lambda>  
self.load_button.clicked.connect(lambda: self.load(self.table.selected))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 389, in load  
self._log_alphafold(models)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 400, in _log_alphafold  
msg = _similarity_table_html(m, query_seq, m.database.id)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/match.py", line 515, in _similarity_table_html  
score, (mseq_gapped, seq_gapped) = nw(mseq, seq, return_seqs = True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 46, in nw  
score, match_list = match(s1.characters, s2.characters, score_match,
score_mismatch,  
AttributeError: 'AtomicStructure' object has no attribute 'characters'  
  
AttributeError: 'AtomicStructure' object has no attribute 'characters'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 46, in nw  
score, match_list = match(s1.characters, s2.characters, score_match,
score_mismatch,  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-16.0.12 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GTX 775M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      System Firmware Version: 433.140.2.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.15f7

Software:

    System Software Overview:

      System Version: macOS 12.6.3 (21G419)
      Kernel Version: Darwin 21.6.0
      Time since boot: 1:39

Graphics/Displays:

    NVIDIA GeForce GTX 775M:

      Chipset Model: NVIDIA GeForce GTX 775M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x119d
      Revision ID: 0x00a2
      ROM Revision: 3782
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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    ChimeraX-Mol2: 2.0
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    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
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Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Zach Pearson Eric Pettersen added
Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → AlphaFold/Blast: Needleman-Wunsch being passed structure, not sequence

Reported by Ulrich Baumann

comment:2 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in tomorrow's daily build (Feb 28, 2023).

Using the AlphaFold panel, pasting in a sequence, pressing Search to run blast against the AlphaFold database and then clicking on a line in the blast results table and loading the structure produces this error. This code was added after ChimeraX 1.5 so only effects the daily builds. The error was from the code that was logging the sequence similarity of the loaded matching structure. I fixed that code passing a chain instead of a structure to the logging code.

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