tamimmurad
commented
11 months ago Hi @azureycy Also, the tmscore threshold is not obvious to what tmscore it is referring because I thought I will use it to limit the output. For example I used the following command: foldseek easy-search ma-asfv-asfvg-156.cif PDB_downloaded/PDB viral_nonviral_results/aln_pdb_nonv_0.3 tmp --alignment-type 1 --tmscore-threshold 0.3 --format-output 'query,target,evalue,qtmscore,ttmscore,alntmscore,' I got the below results: ma-asfv-asfvg-156.cif 7vep_A 4.129E-01 4.045E-01 4.832E-01 4.832E-01 ma-asfv-asfvg-156.cif 8bbe_C 2.854E-01 3.863E-01 3.604E-01 3.604E-01 Then I used the same command with a 0.2 threshould and gave more hits but confusing results that is not matching to any of the alignments tm scores available so it seems it refer to non of them: ma-asfv-asfvg-156.cif 7vep_A 4.129E-01 4.045E-01 4.832E-01 4.832E-01 ma-asfv-asfvg-156.cif 4wsl_A 3.988E-01 3.948E-01 4.508E-01 4.508E-01 ma-asfv-asfvg-156.cif 4pjq_B 3.950E-01 3.415E-01 5.065E-01 5.065E-01 I think the best for now is not to use the threshold and use different format mode to post process the results and pick top hits only
Hi,
Is there any command argument that can just generate the top ten hits in the html/tabular output when using foldseek search? As the command below, I already set the e-value and tmscore-threshold, but some html format outputs still have very long content.
foldseek easy-search input.pdb esmdb out.html tmp -e 1e-5 --alignment-type 1 --tmscore-threshold 0.45 --format-mode 3 --threads 20
Thank you!