source: tags/arb-6.0.5/HELP_SOURCE/oldhelp/pfold_sai.hlp

#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      arb_ntree.hlp
UP      pfold.hlp
UP      glossary.hlp

#Please insert subtopic references  (line starts with keyword SUB)

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE           Create SAI from protein secondary structure

OCCURRENCE      ARB_NT/SAI/Create SAI using/Protein secondary structure

DESCRIPTION

        Takes the currently selected species and searches for the field 'sec_struct'.
        A new SAI is created using the data in this field. A simple input window pops
        up where the default name '[species name]_pfold' for the new SAI can be
        changed.

NOTES

        The import filter 'dssp_all.ift' allows for importing the amino acid
        sequence as well as the protein secondary structure from a dssp file and
        the structure is stored in the field 'sec_struct'. That way, secondary
        structure can be aligned along with the sequence manually and can later
        be extracted to create an SAI.
        
        The import filter 'dssp_2nd_struct.ift' extracts only the protein
        secondary structure which is stored as alignment data. SAIs can simply
        be created from these species with 'Species -> Convert to SAI' in the
        'Species Information' window (see LINK{sp_sp_2_ext.hlp}).
        
        Refer to LINK{arb_import.hlp} and especially LINK{dssp_ift.hlp}
        for detailed information on importing sequences and structures and
        on the DSSP format.

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known