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