diff --git a/fragfold/create_fragment_msa.py b/fragfold/create_fragment_msa.py
index 0d3c18f..9d3ee53 100644
--- a/fragfold/create_fragment_msa.py
+++ b/fragfold/create_fragment_msa.py
@@ -12,6 +12,7 @@ def main(args):
     fragment_name = Path(fragment_a3m).stem
     fragment_start_range = (args.fragment_ntermres_start,args.fragment_ntermres_final)
     fragment_length = args.fragment_length
+    fragment_tile_step = args.fragment_tile_step
     protein_copies = args.protein_copies
 
     protein_range = (args.protein_ntermres,args.protein_ctermres)
@@ -23,6 +24,7 @@ def main(args):
                                                                 protein_range,
                                                                 fragment_start_range,
                                                                 fragment_length,
+                                                                fragment_tile_step,
                                                                 protein_copies)
     else:
         # Create heteromeric interaction MSAs: fragments of protein A + full-length protein B
@@ -37,6 +39,7 @@ def main(args):
                                                                         protein_range,
                                                                         fragment_start_range,
                                                                         fragment_length,
+                                                                        fragment_tile_step,
                                                                         protein_copies)
     with open("a3m_list.txt","w") as file:
         for path in msa_path_list:
@@ -71,6 +74,12 @@ def main(args):
         help="The residue length of the fragments",
         default=30
     )
+    parser.add_argument(
+        "--fragment_tile_step",
+        type=int,
+        help="The tiling step size in aa when generating fragments",
+        default=1
+    )
     parser.add_argument(
         "--protein_a3m_input",
         type=Path,
diff --git a/fragfold/src/colabfold_create_msa.py b/fragfold/src/colabfold_create_msa.py
index bf35122..cb58e79 100644
--- a/fragfold/src/colabfold_create_msa.py
+++ b/fragfold/src/colabfold_create_msa.py
@@ -196,7 +196,7 @@ def verifyProteinRange(protein_range,protein_n_res):
        (protein_range[1] > protein_n_res):
         raise ValueError(f"Provided protein residue range: ({protein_range[0]},{protein_range[1]}) is invalid")
         
-def createIndividualMSAsFullLengthFragment(a3m_path,name,protein_range,fragment_start_range,fragment_length,protein_copies=1):
+def createIndividualMSAsFullLengthFragment(a3m_path,name,protein_range,fragment_start_range,fragment_length,fragment_tile_step,protein_copies=1):
     '''Loads a monomer MSA and creates new MSAs that contain 1) a large section of the monomer and 2) a short fragment of the monomer
     
     Args
@@ -211,6 +211,8 @@ def createIndividualMSAsFullLengthFragment(a3m_path,name,protein_range,fragment_
         an inclusive range defining the range of starting residues for fragments of length `fragment_length`
     fragment_length : int
         the number of residues to take when defining a fragment
+    fragment_tile_step : int
+        the number of residues to step when generating fragments
     '''
     print("Generating MSAs for a monomeric interaction...")
 
@@ -227,7 +229,7 @@ def createIndividualMSAsFullLengthFragment(a3m_path,name,protein_range,fragment_
     except FileExistsError:
         print('Directory already exists, possibly overwriting existing files')
 
-    fragment_start_iter = range(fragment_start_range[0],min(fragment_start_range[1]+1,protein_n_res-fragment_length+2))
+    fragment_start_iter = range(fragment_start_range[0],min(fragment_start_range[1]+1,protein_n_res-fragment_length+2),fragment_tile_step)
     with Pool() as p:
         a3m_out_path_list = p.starmap(createIndividualMSAsFullLengthFragment_starmap,[(a3m_path,fragment_start,fragment_length,dir_name,name,protein_copies,protein_range) for fragment_start in fragment_start_iter])
 
@@ -241,7 +243,7 @@ def createIndividualMSAsFullLengthFragment_starmap(a3m_path,fragment_start,fragm
     createMSA(a3m_path, protein_range, fragment_range, -1, abs_a3m_out_path, protein_copies)
     return abs_a3m_out_path
         
-def createIndividualMSAsFullLengthFragmentHeteromeric(fulllength_a3m_path,fulllength_name,fragment_a3m_path,fragment_name,protein_range,fragment_start_range,fragment_length,protein_copies=1):
+def createIndividualMSAsFullLengthFragmentHeteromeric(fulllength_a3m_path,fulllength_name,fragment_a3m_path,fragment_name,protein_range,fragment_start_range,fragment_length,fragment_tile_step,protein_copies=1):
     '''Loads a monomer MSA and creates new MSAs that contain 1) a large section of the monomer and 2) a short fragment of the monomer
     
     Args
@@ -258,6 +260,8 @@ def createIndividualMSAsFullLengthFragmentHeteromeric(fulllength_a3m_path,fullle
         an inclusive range defining the range of starting residues for fragments of length `fragment_length`
     fragment_length : int
         the number of residues to take when defining a fragment
+    fragment_tile_step : int
+        the number of residues to step when generating fragments
     '''
     print("Generating MSAs for a heteromeric interaction...")
 
@@ -275,7 +279,7 @@ def createIndividualMSAsFullLengthFragmentHeteromeric(fulllength_a3m_path,fullle
     except FileExistsError:
         print('Directory already exists, possibly overwriting existing files')
 
-    fragment_start_iter = range(fragment_start_range[0],min(fragment_start_range[1]+1,fragmentprotein_n_res-fragment_length+2))
+    fragment_start_iter = range(fragment_start_range[0],min(fragment_start_range[1]+1,fragmentprotein_n_res-fragment_length+2),fragment_tile_step)
     with Pool() as p:
         a3m_out_path_list = p.starmap(createIndividualMSAsFullLengthFragmentHeteromeric_starmap,[(fulllength_a3m_path,fragment_a3m_path,fragment_start,fragment_length,dir_name,fulllength_name,fragment_name,protein_copies,protein_range) for fragment_start in fragment_start_iter])