Similar Structures tool: tried to search Alphafold DB using BLAST

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-14.7-arm64-arm-64bit
ChimeraX Version: 1.9.dev202410191420 (2024-10-19 14:20:42 UTC)
Description
Similar Structures tool: tried to search Alphafold DB using BLAST

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

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

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

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html; ui dockable false "Help Viewer"

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html; ui dockable false "Help Viewer"

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

> alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-
> channel.html; ui dockable false "Help Viewer"; windowsize 600 800

executed startup.cxc  
UCSF ChimeraX version: 1.9.dev202410191420 (2024-10-19)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> usage foldseek

foldseek chain [database database] [trim trim] [alignmentCutoffDistance a
number] [saveDirectory name of a folder to save/write; a name of 'browse' will
bring up a file browser] [wait true or false] [showTable true or false]  
— Search for proteins with similar folds using Foldseek web service  
database: one of afdb-proteome, afdb-swissprot, afdb50, or pdb100  
trim: a collection of one of chains, ligands, or sequence or true or false  

> version

UCSF ChimeraX version: 1.9.dev202410191420 (2024-10-19)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open 1gvz format mmcif fromDatabase pdb

1gvz title:  
Prostate Specific Antigen (PSA) from stallion seminal plasma [more info...]  
  
Chain information for 1gvz #1  
---  
Chain | Description | UniProt  
A | KALLIKREIN-1E2 | KLK2_HORSE 16-246  
  
Non-standard residues in 1gvz #1  
---  
ACT — acetate ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
38 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show "Similar Structures"

> foldseek /A

Found 827 similar structures to 1gvz #1/A in pdb database using foldseek, name
fs1  

> open 1qqu

Summary of feedback from opening 1qqu fetched from pdb  
---  
note | Fetching compressed mmCIF 1qqu from http://files.rcsb.org/download/1qqu.cif  
  
1qqu title:  
Crystal structure of porcine β trypsin with bound acetate ion [more info...]  
  
Chain information for 1qqu #2  
---  
Chain | Description | UniProt  
A | BETA TRYPSIN | TRYP_PIG 16-245  
  
Non-standard residues in 1qqu #2  
---  
ACT — acetate ion  
CA — calcium ion  
  
Alignment of 1qqu chain A to query has RMSD 0.904 using 177 of 223 paired
residues within cutoff distance 2.0  

> similarstructures traces

827 traces showing 148066 residues with 22230 far or short segment residues
hidden  

> usage similarstructures

Subcommands are:

  * similarstructures close
  * similarstructures cluster
  * similarstructures fetchcoords
  * similarstructures fromblast
  * similarstructures ligands
  * similarstructures list
  * similarstructures open
  * similarstructures pairing
  * similarstructures scrollto
  * similarstructures seqalign
  * similarstructures sequences
  * similarstructures traces

  

> sequence search #1/A

Found 1407 similar structures to 1gvz #1/A in pdb database using mmseqs2, name
mm1  

> sequence blast #1/A database afdb

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 238, in _search  
run(self.session, cmd)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.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/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/blast_search.py", line 32, in
sequence_blast  
job = blastprotein(session, chain, database = database, cutoff =
evalue_cutoff,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/cmd.py", line 88, in blastprotein  
job = BlastProteinJob(  
^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/job.py", line 49, in __init__  
self.setup(seq, atomspec, **kw)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/job.py", line 96, in setup  
version = CurrentDBVersions[self.database]  
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
KeyError: 'afdb'  
  
KeyError: 'afdb'  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/blastprotein/job.py", line 96, in setup  
version = CurrentDBVersions[self.database]  
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK1F3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.1.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7 (23H124)
      Kernel Version: Darwin 23.6.0
      Time since boot: 3 hours, 45 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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[Tom Goddard]

Fixed.

Oops. Apparently I never retested similar structures blast against alphafold database after I changed the "database" option value "alphafold" to "afdb". The blast alphafold search takes I think 5 to 10 minutes. One of the main advantages of mmseqs2 is that it is 10x faster doing that search. I think blast search capability in similar structures should be rarely used, and I included it for completeness. But of course it is supposed to work!