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