-NAN Output for LDDT Score

steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

https://foldseek.com

GNU General Public License v3.0

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-NAN Output for LDDT Score #233

Open Dylan-Barcelos opened 5 months ago

Dylan-Barcelos commented 5 months ago

Hello, I ran foldseek easy-search for a collection of structures and had the last two columns as structural alignment scores (qtmscore, lddt). When I look through the file there are a number of instance where all the other scores are numeric but the LDDT score is a -NAN value. What could be causing this?

milot-mirdita commented 5 months ago

Could you please upload the full output of foldseek and ideally also the query structure?

Dylan-Barcelos commented 5 months ago

log.txt

I attached the log file for this particular run. The query structure is defined by a 12A local region around a selected ligand to focus the local alignments of foldseek around a ligand binding zone.

milot-mirdita commented 5 months ago

Is it possible to upload the PDB file? This looks very fragmented, maybe we have a bug with residue index jumps.

Dylan-Barcelos commented 5 months ago

4occ_selected.pdb.zip I added the pdb file as a .zip attachment.