Hi, 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.

Here is the input file, fix_positions.ali >P1;1abc sequence:1abc:1::10:: : :-1.00:-1.00 FGAVAFATTT* >P1;1def sequence:1def: :: :: : :-1.00:-1.00 AVAFATTT* >P1;_fix_pos sequence:x: :: :: : :-1.00:-1.00 0000000000*

Following is the .py file. I've removed the comments but it's taken directly from the manual log.verbose() env = environ() aln = alignment(env, file='fix_positions.ali', align_codes=('1abc', '1def', '_fix_pos')) aln.salign(fix_offsets=(0, 1000, 2000, 3000, 4000), gap_penalties_2d=(0, 0, 0, 0, 0, 0, 0, 0, 0), # Any values are # possible here local_alignment=False, # Local alignment works, too gap_penalties_1d=(-600, -400)) # This is best with the default value # of gap_penalties_2d aln.write(file='fix_positions_salign.pap', alignment_format='PAP')

If I run this, I will get an alignment of: _aln.pos 10 1abc FGAVAFATTT 1def --AVAFATTT _consrvd ********

But suppose I want to force the first Alanine in 1abc to be aligned with the 2nd Alanine in 1def. I want modeller to align all other residues normally (as it normally would without any fix_offsets).

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*

I've been playing around with it but can't seem to get it work correctly.

To ask the question a different way, given two sequnces, A and B, how does one tell Modeller the residue #X of sequence A must be aligned with residue #Y of sequence B.

Thank you, Jim Fonseca