Thanks Ben!
I modified the script accordingly:
# Make a pairwise alignment of two sequences aln = alignment(env, file='template.ali') aln.salign(overhang=5, gap_penalties_1d=(-450, -50), alignment_type='pairwise', output='ALIGNMENT') aln.write(file='template.pir', alignment_format='PIR') aln.write(file='template.pap', alignment_format='PAP')
It worked beautiful.
On Wed, Nov 13, 2013 at 4:34 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 11/13/13 8:28 AM, Amjad Farooq wrote: > >> I am noticing that Modeller does not do a good job when it comes to >> sequence alignment of short peptides or DNA sequences. >> > > You're not required to use Modeller to make modeling alignments - as long > as you can make alignment files in the PIR format Modeller wants, you can > use any package (including ClustalW). > > That said, by default Modeller's alignment methods use global alignment > and so try to align the termini, since this is typically what you want for > modeling. You can adjust the overhang parameter to discourage this > behavior, or use local alignment. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >