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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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Foldseek Webserver - JSON downloaded output does not contain RMSD or TM score values #307

Open kamurani opened 2 months ago

kamurani commented 2 months ago

Expected Behavior

After performing a search and choosing the All data Reloadable JSON file option to download the search results, there is no TMscore or RMSD values JSON file. The values are visible when clicking on the 'alignment' view per hit, which can only be done manually (there is no way to programmatically access this data). This data should be contained along with every other per-row value in the JSON output.

Steps to Reproduce (for bugs)

Run foldseek search, download JSON

milot-mirdita commented 2 months ago

RMSD and TM-Score are computer on the fly with a webassembly based tmalign when the alignment panel is opened. So we don’t have the information available for the JSON.

kamurani commented 2 months ago

Thanks for your reply.

Do you know any more details about which version of the TM-align program is used? And on which residues? I'm guessing the reported score is on the subset of coordinates that are in the alignment (i.e. query alignment start-end)