diff --git a/ImageD11/nbGui/S3DXRD/pbp_3_refinement.ipynb b/ImageD11/nbGui/S3DXRD/pbp_3_refinement.ipynb
index d02dcddd..342473c6 100755
--- a/ImageD11/nbGui/S3DXRD/pbp_3_refinement.ipynb
+++ b/ImageD11/nbGui/S3DXRD/pbp_3_refinement.ipynb
@@ -202,14 +202,13 @@
     "\n",
     "y0 = 0.0\n",
     "ybeam = 0.0\n",
-    "fpks = 0.95\n",
     "hkl_tol_origins = 0.05\n",
     "hkl_tol_refine = 0.1\n",
     "hkl_tol_refine_merged = 0.05\n",
     "ds_tol = 0.006\n",
     "ifrac = 6e-3\n",
     "\n",
-    "refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, fpks=fpks, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str)"
+    "refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str)"
    ]
   },
   {
@@ -395,7 +394,7 @@
     "        pmap = PBPMap(ds.pbpfile)\n",
     "        pmap.choose_best(min_unique)\n",
     "        \n",
-    "        refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, fpks=fpks, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str)\n",
+    "        refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str)\n",
     "        \n",
     "        refine.setmap(pmap)\n",
     "        refine.setpeaks(cf_2d)\n",
diff --git a/ImageD11/nbGui/S3DXRD/tomo_3_refinement.ipynb b/ImageD11/nbGui/S3DXRD/tomo_3_refinement.ipynb
index 8e7bdafa..03ba4685 100755
--- a/ImageD11/nbGui/S3DXRD/tomo_3_refinement.ipynb
+++ b/ImageD11/nbGui/S3DXRD/tomo_3_refinement.ipynb
@@ -231,14 +231,13 @@
     "\n",
     "y0 = grainsinos[0].recon_y0\n",
     "ybeam = 0.0\n",
-    "fpks = 0.9\n",
     "hkl_tol_origins = 0.05\n",
     "hkl_tol_refine = 0.1\n",
     "hkl_tol_refine_merged = 0.05\n",
     "ds_tol = 0.004\n",
     "ifrac = 7e-3\n",
     "\n",
-    "refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, fpks=fpks, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str)"
+    "refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str)"
    ]
   },
   {
@@ -442,7 +441,7 @@
     "        pmap = tensor_map.to_pbpmap(z_layer=0, default_npks=20, default_nuniq=20)\n",
     "        pmap.choose_best(1)\n",
     "\n",
-    "        refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, fpks=fpks, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str)\n",
+    "        refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str)\n",
     "        \n",
     "        refine.setmap(pmap)\n",
     "        refine.setpeaks(cf_2d)\n",
diff --git a/ImageD11/nbGui/S3DXRD/tomo_3_refinement_minor_phase.ipynb b/ImageD11/nbGui/S3DXRD/tomo_3_refinement_minor_phase.ipynb
index 18fca870..b1625d65 100755
--- a/ImageD11/nbGui/S3DXRD/tomo_3_refinement_minor_phase.ipynb
+++ b/ImageD11/nbGui/S3DXRD/tomo_3_refinement_minor_phase.ipynb
@@ -319,7 +319,6 @@
     "\n",
     "y0 = grainsinos[0].recon_y0\n",
     "ybeam = 0\n",
-    "fpks = 0.9\n",
     "hkl_tol_origins = 0.05\n",
     "hkl_tol_refine = 0.1\n",
     "hkl_tol_refine_merged = 0.05\n",
@@ -328,7 +327,7 @@
     "forref = [0, 2, 3, 4, 5, 6, 7, 8, 10, 12, 13]\n",
     "phase_str = minor_phase_str\n",
     "\n",
-    "refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, fpks=fpks, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str, forref=forref)"
+    "refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str, forref=forref)"
    ]
   },
   {
@@ -562,7 +561,7 @@
     "        pmap = tensor_map.to_pbpmap(z_layer=0, default_npks=20, default_nuniq=20)\n",
     "        pmap.choose_best(1)\n",
     "\n",
-    "        refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, fpks=fpks, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=minor_phase_str, forref=forref)\n",
+    "        refine = PBPRefine(dset=ds, y0=y0, ybeam=ybeam, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=minor_phase_str, forref=forref)\n",
     "        \n",
     "        refine.own_filename = os.path.splitext(refine.own_filename)[0] + f'_{phase_str}.h5'\n",
     "        refine.icolf_filename = os.path.splitext(refine.icolf_filename)[0] + f'_{phase_str}.h5'\n",