#       main topics:
UP      arb.hlp
UP      arb_ntree.hlp
UP      pfold.hlp
UP      glossary.hlp

#       sub topics:

# format described in ../help.readme


TITLE		Create pfold SAI

                Import protein secondary structure and convert into SAI.

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

DESCRIPTION

	Takes the currently LINK{selected.hlp} 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 using 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
