I'm trying to figure out how to use fix_offsets with align2d. Please follow this example, based on
the
salign() example (under the 'Alignments using external restraints subsection') in the manual.
See the example input alignment examples/salign/fix_positions.ali
Like the documentation says, the final pseudo sequence '_fix_pos' can
contain 5 'residue' types: 0 through 4 (blanks are treated as 0). The
alignment matrix is offset (i.e. an alignment at that position is made
more favorable) if you put in a non-zero integer.
So I want something that would _probably_ look like this:
_aln.pos 10
1abc FGAVAFATTT
1def AVA--FATTT
_consrvd ********
The only thing that matters is that the first A in 1abc is forced to align with the 2nd A in 1def.
How do I get these particular Ala residues to be forced to align using _fix_pos input in the
alignment
file? Specifically, what would I need to put in place of the zeros below?
P1;_fix_pos
sequence:x: :: :: : :-1.00:-1.00
0000000000*
Just construct your input alignment such that it has the desired A-A
alignment in the third column, and then put 4 in the third column of the
_fix_pos sequence.