[modeller_usage] Error using local_alignment=True in salign

[David Abia <>]

Dear Modeller users,

I'm trying to force a local alignment while using salign function in 
mod9.15, and it fails with error:

"modeller.ModellerError: align_l_251E> MATRIX_OFFSET probably has an 
invalid value:        0.0000"

My script ( mod-3nnt-prim.cons-aln.py ):

from modeller import *
env = environ()
aln = alignment(env)
m = model(env, file='./tmp-NmArZQ.pdb', model_segment=('FIRST:A', 'LAST:B'))
aln.append_model(m, atom_files='./tmp-NmArZQ.pdb', align_codes='3nnt_x')
aln.append( file='./tmp-q4VfPF.fasta',  alignment_format='FASTA', 
align_codes='prim.cons')
aln.salign(local_alignment=True)
aln.write(file='mod-3nnt-prim.cons.pir')

The output:

Traceback (most recent call last):
  File "mod-3nnt-prim.cons-aln.py", line 8, in ?
    aln.salign(local_alignment=True)
  File "/usr/lib/modeller9.15/modlib/modeller/alignment.py", line 395, 
in salign
    nsegm, matrix_offset_3d, break_break_bonus)
_modeller.ModellerError: align_l_251E> MATRIX_OFFSET probably has an 
invalid value:        0.0000

The error comes from a call to a function:

retval = func(self.modpt, ... , local_alignment, .... , nsegm, 
matrix_offset_3d, break_break_bonus)

that is defined as:

func = _modeller.mod_salign

If I remove the option "local_alignment=True", it runs flawlessly.

Any idea about what can be happening?

Thanks in advance,

David.