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[modeller_usage] Question about Search for templates command...



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:

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
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221