hh-suite
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soedinglab
Remote protein homology detection suite.
Dear all, I want to use hhblits to build my own database(1,040,000seqs). I followed the tutorial "Building customized databases", and the second step is to build an MSA with HHblits...
## Expected Behavior HHblits command to generate MSAs in AlphaFold2 from BFD and UniRef30 databases should complete without errors. ## Current Behavior The hhblits command in AlphaFold2 often fails with...
Hi, While I was trying to download hhsuite for my conda environment, I get an error message. I tried to change my channels settings but it did not work. I...
I put one chain from a PDB into my library, then run either HHBLits or HHSearch against another homologous chain with indels and the indels do not align between query...
I have tried to create an updated version of the PDB70 database myself to include the proteins added since march, but because the uniclust30 database isn't updated either, I'd have...
I'm trying to create a custom database, but find that I am getting many fewer entries in _a3m.ff{data,index} and _hhm.ffindex after running ffindex_order than are present in the input files....
Hi, I'm trying to use hhsearch with a customized database. Both query and database alignments represent an entire family of homologs (there is no seed sequence). Hence, I reckon that...
**My steps:** conda install -c conda-forge -c bioconda hhsuite hhblits -i A.fasta -d pdb70 -oa3m A.a3m hhmake -i A.a3m -o A.hhm **My question:** Can *and NULL in the generated hhm...
Following header changes in gcc 13, hh-suite fails to build with the following errors: In file included from //src/a3m_compress.cpp:8: //src/a3m_compress.h:37:37: error: ‘uint16_t’ has not been declared 37 | void writeU16(std::ostream&...
I am getting the following error while running alphafold : Started HHblits query I0811 15:48:12.553200 22849205610304 utils.py:40] Finished HHblits query in 0.134 seconds E0811 15:48:12.553327 22849205610304 hhblits.py:138] HHblits failed. HHblits...
