Re: [modeller_usage] Problem in SEQUENCE_SEARCH

[Modeller Caretaker <>]

On Tue, Oct 14, 2003 at 05:27:57PM -0300, Jorge Hernanez Fernandez wrote:
>    Is any expertise in the use of the command SEQUENCE_SEARCH ?
> All the time I use, the program stop trying to read the ?CHAINS_all.seq? file.
> Is any kind of problem in the file? I will appreciate any help in this task.
> Thanks in advance:
> 
>                       Jorge H.F.
> 
> Top file is:
> 
> 
> INCLUDE
> SET OUTPUT_CONTROL = 1 1 1 1 1
> SET ATOM_FILES_DIRECTORY = '/export/db/pdb'          
> SET OUTPUT = 'SHORT' # 'LONG'
> SET SIGNIF_CUTOFF = 8 3
> SET SEARCH_RANDOMIZATIONS = 10
> SET STOP_ON_ERROR = 2
> SET FAST_SEARCH = ON
> SET DATA_FILE = ON
> CALL ROUTINE = 'sequence_srch', SEGFILE = 'DNApol.txt', SEQUENCE = 'DNApol'

SEQUENCE_SEARCH will do a alignment between your given sequence and
every one of the proteins listed in SEARCH_CHAINS_LIST. Since you
haven't set this list in your top file, it will use the default set in
top.ini (i.e. CHAINS_3.0_40_XN.cod). Since there are a lot of protein
codes in there, the search will take a very long time. You probably want
to create a more targeted list of proteins to compare against. See
examples/all-steps/search.top for an example (this uses
'SET SEARCH_CHAINS_LIST' to give a shorter list of protein codes to the
search).

	Ben Webb, Modeller Caretaker
-- 
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