setting hhsuite problem- pls help

Question

[Xylanaser]

Hi can someone help me ? what i must do to set hhsuite.

1. I download files and dbs (i cant find uniprot20 ? is this needed? i downloaded scop , pdb, pfam and uniclust30)

2. installed hhsuite from dpkg (i use ubuntu)

3. I dont know now - how to set paths for hhsuite (i set some paths to other programs earlier , but here i cant cope :( )

can u give me advise what to do?

Best

Answer 1

[Joe]

My previous answer here, might help.

It has been improved in recent versions but it can be tricky to install.

I haven't tried it this way, but it appears to be available in conda, so try installing it through that (normally super easy!).

See how you get on, at the moment your question is a bit vague. Come back to us if you have some specific errors etc.

[Xylanaser]

hmmm really thanks. I used conda as u said but i dont know how to set path to dbs :) i willl try just by inputin paths in terminal (hhblits -i query -db <path> ...) Im confused what to do =, but ill try later with that... thanks again

[Joe]

Try providing the path directly to one of the *.ffdata files for one of the databases using hhsearch, since it only requires a single file. hhblits, if I recall correctly, requires that you only provide the basename of the database (without any extensions) since it relies on multiple files.

For instance, try:

hhsearch -i <protein.fasta> -db /path/to/pdb/pdb70_hhm.ffdata

and see if that works.

[Xylanaser]

• 18:44:06.113 ERROR: Could not open file '/usr/share/hhsuite/data/context_data.crf'

almost work :) but this. I have checked this file does not exist What is in that folder : context_data.lib and cs219.lib

[Xylanaser]

ok, it exist but in anaconda pkgs ,maybe it my fault becouse i've installed hhsuite earlier from dpkg and one of paths is wrong :(

[Joe]

Yes you will have conflicting versions now.

Judging by /usr/share/ I would guess that is a problem with the dpkg installed version.

What is the output of which -a hhsearch ?

[Xylanaser]

• /usr/bin/hhsearch
• /home/mar/anaconda3/bin/hhsearch

double path

[GenoMax]

Try export PATH=/home/mar/anaconda3/bin/:$PATH. That should pick up the conda hhsearch before the /usr/bin one.

[Xylanaser]

thanks for help, I solve it :) here's my solution: i've installed hhsuite from dpkg and have paths for scripts , next download / clone from git and JUST (!) set variables to hhsuite folder (because i cant find folder with all files after dpkg... ) And it works :) cheers