jf163201@ohio.edu wrote: > 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.
Ben Webb, Modeller Caretaker