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Hi,
I am trying to turn clusters of nucleotide sequences into profiles.
I did the following:
mmseqs cluster Athself AthselfDB /tmp -c 0.5
mmseqs createseqfiledb Athself AthselfDB AthselfDBSEQ --…
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I get this runtime error while running all vs all.
I assume that I'm using the wrong version of Jax or something?
```
create_ppi_all_vs_all.sh broken_1RWY.fa $HHBLITS 0.5 outdir
Writing fas…
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Hi,
I'm new to bioinformatics and I am interested to use prospr to predict the structure of my protein of interest. I'd like to use this space to figure out how to actually run this software.
S…
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I have two profiles within the pfam database: PF00336.20 and PF17919.3. Querying the database using **hhsearch** with PF00336 hmm as a query I got mapping to PF17919:
`ffindex_get pfam_hhm.ffdata pfa…
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In the Usage, there is code like
`seq = torch.randint(0, 21, (1, 128)).cuda()`
`msa = torch.randint(0, 21, (1, 5, 64)).cuda()`.
If I have a a3m msa file, how to encode the file to this tensor? And …
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I find that the most format EM maps is .map, but this software needs .mrc. Is the software supports .maps format?
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here is the error:
`./input_prep/make_ss.sh: line 18: 11775 Aborted (core dumped) psipred $ID.mtx $DATADIR/weights.dat $DATADIR/weights.dat2 $DATADIR/weights.dat3 > $ID.ss`
I am …
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I am building a custom database according the instructions in the user guide. I would like to understand more specifically how cstranslate converts an alignment to an abstract state alphabet. In parti…
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Hello
I'm working on ConSurf in Nir Ben-Tal's laboratory. The ConSurf website uses a local installation of hhsuite. It has worked for many years but lately it stopped working. In order to see where…
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I want to generate features for a protein complex with a modified version of the `example/run_fea_gen.sh` script:
```
#!/bin/bash
# An example script of feature generation. This heavily depeneden…