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



Sergio Garay wrote:
I'm following the modeller tutorial to make a search for templates but with no success.
...
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

You must be using a very old version of the tutorial. SEQUENCE_SEARCH is an old and inefficient search mechanism, and is not used any more in the online tutorial; use profile.build() instead, as demonstrated at http://salilab.org/modeller/tutorial/basic.html

If you really want to use SEQUENCE_SEARCH, you must let it run for a very long time with modern sequence databases - probably more than 3-4 hours.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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