#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
