HHpred installation problem
Entering edit mode
5.2 years ago
Xylanaser ▴ 80

Hello. I am trying to install hhpred

I have compiled HHsuite and add to .bashrc:

export PATH="/home/xyl/hh-suite/build//bin:/home/xyl/hh-suite/build/scripts:$PATH"

Everything works fine (I have downloaded scop70, pfam.32, uniclust30 and pdb70latest)

Now i want to install hhpred , but im little cofused

  • 1) install the hh-suite library #done
  • 2) download hhpred databases:

    hhpred needs hhm, a3m and pdb files for each template, all in the same folder goto http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/ and download the latest pdb70.a3m.tar.gz, pdb70.hhm.tar.gz, pdb70*.a3m.tar.gz and extract them into your hhpred database folder enter the path to the database into the config.pm file in the "lib" folder (entry: _pdbdir) enter the path to the uniprot database into the config.pm file in the "lib" folder (entry: _uniprot20)

  • create a folder called "db" in your database folder, open a terminal, change into this folder and call "cat ../*.hhm > pdb.hhm" pdb_latest contains:

    • pdb70.cs219, pdb70.cs219.sizes, pdb70_a3m.ffdata, pdb70_a3m.ffindex, pdb70_a3m_db, pdb70_a3m_db.index, pdb70_clu.tsv, pdb70.cs219.ffdata, pdb70.cs219.ffindex, pdb70.cs219.ffdata, pdb70_hhm.ffdata, pdb70_hhm.ffindex, pdb70_hhm_db, pdb70_hhm_db.index, pdb_filter.dat

there is no one file with enlargement '.hhm' so i can not call "cat ../*.hhm > pdb.hhm"

can you advice me what to do?

best, xylanaser

protein hhpred • 2.3k views
Entering edit mode

Did you figure where to download the following files:

pdb70.a3m.tar.gz, and pdb70.hhm.tar.gz

I'm encountering the same issue as you did, with little support from soeding Lab GitHub (most people involved in this have graduated and busy with their current jobs)

Any help would be deeply appreciated!

Entering edit mode

Hey. No :(. They did not answer me... If you learn something, I'm asking for help too. Cheers

Entering edit mode

latest pdb70 is here http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/ they update it (I do not have the latest one) , I can not find *.hmm file only pdb70_hhm.ffdata, pdb70_hhm.ffindex, pdb70_hhm_db, pdb70_hhm_db.index. I do not checked old releases: http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/


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