I've been running HHPRED, and following error message appears:
- Could find neither hhm_db nor a3m_db!
How can I configure these variables on HHPRED? Github page [1] says nothing about it!!
[1] https://github.com/soedinglab/hh-suite/tree/master/scripts/hhpred
Hello,
You need to download your preferred databases from the address "http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/", such as pdb70 and scop90, etc., according to your needs.
PS1: hhm_db and a3m_db mean database files in hhm and a3m formats, respectively
PS2: Take a look at their official website "https://toolkit.tuebingen.mpg.de/hhpred" for more information.
Hello Jinchao,
I've downloaded all required database files as stated in [1], and also created a file called pdb.a3m, following similar procedure as stated in [1], and error still occurs.
[1] https://github.com/soedinglab/hh-suite/tree/master/scripts/hhpred
Did you try to install only HHpred? You need to follow the page of https://github.com/soedinglab/hh-suite rather than the page of scripts/hhpred.
If you hadd already installed hhsuite and built the database correctly, did you try to use -d option to tell the program the path of your build database?
I had no single problem when installing hhsuite before.
"Did you try to install only HHpred?"
No, I didn't.
"You need to follow the page of https://github.com/soedinglab/hh-suite rather than the page of scripts/hhpred."
That's what I've done. HH-Suite installation worked as expected, and I've configured databases as github page guides.
Check if your HHsearch works properly. I see this is the only place where hhm database is used in hhpred.pl.
Finally got to solve this issue :-D but used a different way:
First, I've downloaded pdb70_06Sep14 on link attached (index of dbs used by hhsuite), extracted to a folder, and renamed some files, while making some links. Final result of folder is in attached image.
Then, I followed step two from this guide:
https://github.com/soedinglab/hh-suite/tree/master/scripts/hhpred
After that, I've opened hhpred.pl source code, changing line 174 for this instruction:
my $pdbdb = "$pdbdir/pdb70_06Sep14/pdb70";
This modifications changes reference from "db/pdb.hhm" to "$pdbdir/pdb70_06Sep14/pdb70", in which $pdbdir stands for directory specified in lib/config.pm, in hhpred directory.
______________________________ _____________________
For discover all of this, I've investigated before hhsearch source code, discovering that hhsearch searches into given -d param for ffdata and ffindex files.
http://wwwuser.gwdg.de/%7Ecompbiol/data/hhsuite/databases/hhsuite_dbs/
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