Re: [modeller_usage] fix_offsets to align certain residues

[Modeller Caretaker <>]

 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
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