Comments (4)
milot-mirdita
commented on June 2, 2024
This is a bit of a foot-gun. The --tmscore-threshold is not taken into account in the 3Di+AA alignment mode (2). If you want to use that you have to use the tmalign alignment mode (1).
In the 3Di+AA mode, you have to filter the result file afterwards (e.g., with awk, etc.)
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rothita
commented on June 2, 2024
Ok, I had a feeling I'm missing something. Thanks!
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martin-steinegger
commented on June 2, 2024
I added support for TMscore filtering into 3Di+AA as well. So the flag should work now as expected.
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rothita
commented on June 2, 2024
I added support for TMscore filtering into 3Di+AA as well. So the flag should work now as expected.
Amazing, Thanks!
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Related Issues (20)
- Backbone only search returns no hit. HOT 4
- easy-search hangs on scop40 test HOT 9
- precomputed pdb lookup and sequence don't line up HOT 1
- `--taxon-list` option not accepting multiple taxonomy IDs correctly HOT 5
- Can't find exact match in PDB HOT 2
- 3di for multi-chain protein HOT 2
- Comparison of specified structure fragments HOT 1
- Job kept being stucked in the pending state HOT 7
- How to conduct clusters based on global structures instead of local substructures? HOT 1
- Create human-readable taxonomy lookup table from precomputed database HOT 3
- Potential permission issue when trying to create foldseek db HOT 1
- Error std::out_of_range when creating database with specific cif files HOT 4
- Cannot use createdb to merge two existing db HOT 1
- (core dumped) "$MMSEQS" createcomplexreport "${QUERY}" "${TARGET}" "${SCORECOMPLEX_RESULT}" "${REPORT}" ${REPORT_PAR} HOT 18
- No 3D alignment shown in webserver viewer HOT 9
- Retrain Foldseek's VQ-VAE and compile it with the main program. HOT 1
- How to convert the 3D descriptors back to PDB file? HOT 3
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- How to download AFDB clusters? HOT 3
- Input taxonomy database is missing when using createdb HOT 1
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