Clustered at 95% identity: pdb_95.cod.gz (PDB codes of cluster representatives) pdb_95.grp.gz (PDB codes in each cluster) 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
-- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina
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