matching_residues missing placeholder compared to query_residues

[asliyuksek]

Hi,

In some of my outputs, query_residues has one more entry than matching_residues.

I ran the command below:

folddisco query -i index/mouse -q query/mouse_motifs.txt -t 20 --tm-score 0.25 --rmsd 3.5 --header --format-output qid,tid,node_count,tm_score,idf,rmsd,matching_residues,query_residues

Example output:

qid        tid         node_count  tm_score  idf       rmsd    matching_residues                                      query_residues
query.pdb  target.pdb  11          0.2692    356.7002  3.0368  A196,A215,_,A231,A232,A233,A205,A240,A242,A243,A244,A246,_  A545,A564,A574,A580,A581,A582,A583,A584,A591,A592,A593,A595,A632,A635

Since _ is documented as the placeholder for no match, I expected matching_residues and query_residues to stay aligned and have the same number of comma-separated entries. In this example, matching_residues has 13 entries and query_residues has 14 entries. Is this expected, or could it be an output inconsistency?

[khb7840]

Could you provide the problematic query with me to fix the error?

[asliyuksek]

The problematic query is:

1q43.pdb A545,A564,A574,A580,A581,A582,A583,A584,A591,A592,A593,A595,A632,A635

One example output row from this query is:

tid: AF-Q61410.pdb
matching_residues:
A196,A215,_,A231,A232,A233,A205,A240,A242,A243,A244,A246,_
query_residues:
A545,A564,A574,A580,A581,A582,A583,A584,A591,A592,A593,A595,A632,A635

Here, matching_residues has 13 entries, while query_residues has 14 entries.

[khb7840]

Thanks for reporting this. I find this as an error. I'm investigating what's the cause.