diff --git a/build_modeller.py b/build_modeller.py
index e7c4c74..0cf7c56 100755
--- a/build_modeller.py
+++ b/build_modeller.py
@@ -86,15 +86,35 @@ class PDBModeler:
         aln.append_model(mdl, align_codes=self.structure, atom_files=self.structure_file.as_posix())
         aln.append(file=self.ali_file.as_posix(), align_codes=self.sequence)
         aln.align2d()
-        aln.write(file=(self.outdir / 'alignment.ali').as_posix(), alignment_format='PIR')
-        aln.write(file=(self.outdir / 'alignment.pap').as_posix(), alignment_format='PAP')
+        aln.write(file=(self.outdir / 'alignment1.ali').as_posix(), alignment_format='PIR')
+        aln.write(file=(self.outdir / 'alignment1.pap').as_posix(), alignment_format='PAP')
+
+        # save alignment in FASTA format
+        aln.write(file=(self.outdir / 'alignment1.fasta').as_posix(), alignment_format='FASTA')
+        slice_fasta = PDBModeler.align_sequences(self.outdir / 'alignment1.fasta')
+        slice_ali = self.outdir / 'alignment_slice.ali'
+        fx = pyfastx.Fasta(slice_fasta.as_posix(), build_index=True)
+        assert len(fx) == 1, "FASTA file should contain only one sequence"
+        PDBModeler.write_ali(slice_ali, fx[0].name, fx[0].seq)
+
+        env2 = Environ()
+        mdl2 = Model(env2, file=self.structure_file.as_posix(), model_segment=(f'FIRST:{self.chain}', f'LAST:{self.chain}'))
+        aln2 = Alignment(env2)
+        aln2.append_model(mdl2, align_codes=self.structure, atom_files=self.structure_file.as_posix())
+        aln2.append(file=slice_ali.as_posix(), align_codes=self.sequence)
+        aln2.align2d()
+        aln2.write(file=(self.outdir / 'alignment2.ali').as_posix(), alignment_format='PIR')
+        aln2.write(file=(self.outdir / 'alignment2.pap').as_posix(), alignment_format='PAP')
 
         log.verbose()
 
+        # choose ali file
+        fix_ali_file = self.outdir / 'alignment2.ali' if (self.outdir / 'alignment2.ali').exists() else self.outdir / 'alignment1.ali'
+
         env3 = Environ()
         env3.io.atom_files_directory = ['.']
         loop_model = LoopModel(env3,
-                               alnfile=(self.outdir / 'alignment.ali').as_posix(),
+                               alnfile=fix_ali_file.as_posix(),
                                knowns=self.structure,
                                sequence=self.sequence,
                                loop_assess_methods=(assess.DOPE, assess.GA341))
@@ -151,6 +171,13 @@ class PDBModeler:
             if output.get('failure') is None:
                 model_files.append(Path(output.get('name')))
         return model_files
+    
+    @staticmethod
+    def write_ali(ali_file: Path, description: str, sequence: str):
+        with open(ali_file, 'w') as f:
+            f.write(f'>P1;{description}\n')
+            f.write(f'sequence:{description}:::::::0.00: 0.00\n')
+            f.write(f'{sequence}*')
 
     def fasta_to_ali(self) -> Path:
         if not self.outdir.exists():
@@ -162,12 +189,7 @@ class PDBModeler:
 
         fx = pyfastx.Fasta(self.fasta_file.as_posix(), build_index=True)
         assert len(fx) == 1, "FASTA file should contain only one sequence"
-
-        with open(ali_file, 'w') as f:
-            f.write(f'>P1;{self.sequence}\n')
-            f.write(f'sequence:{self.sequence}:::::::0.00: 0.00\n')
-            f.write(f'{fx[0].seq}*')
-
+        PDBModeler.write_ali(ali_file, self.sequence, fx[0].seq)
         return ali_file
 
 if __name__ == "__main__":