Hi

I'm following the modeller tutorial to make a search for templates but with no success. May be I'm doing something wrong. Below I detail what I did:

1) download the supplemental files:

- All PDB sequences: pdball.pir.gz http://www.salilab.org/modeller/downloads/pdball.pir.gz - Clustered at 95% identity: pdb_95.cod.gz http://www.salilab.org/modeller/downloads/pdb_95.cod.gz(PDB codes of cluster representatives) pdb_95.grp.gz http://www.salilab.org/modeller/downloads/pdb_95.grp.gz(PDB codes in each cluster) pdb_95.pir.gz http://www.salilab.org/modeller/downloads/pdb_95.pir.gz(sequences of cluster representatives)

2) I unpack them into the directory where Modeller should find them: /usr/lib/modeller9v7/modlib. In this point, I have a doubt: in the tutorial said that I should replace the files: CHAINS_3.* with the downloaded before. But I did not find them, at least in that directory. Anyway I renamed the files accordingly the tutorial as:

pdball.pir to CHAINS_all.seq pdb_95.cod to CHAINS_3.0_40_xn.cod

With these modifications I run seqsearch.top and apparently it worked, but after many (3-4) hours I stopped it. it never writes any line in the log file.

seqsearch.top file used as input. SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'TvLDH.ali' READ_SEQUENCE_DB SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON

Any help will be appreciated.

Sergio