cleaning up the rewire example

Author: sokrypton

af/examples/partial_hallucination_rewire.ipynb

@@ -34,8 +34,6 @@
         "  pip -q install git+https://github.com/sokrypton/ColabDesign.git\n",
         "  mkdir params\n",
         "  curl -fsSL https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar | tar x -C params\n",
-        "  for W in openfold_model_ptm_1 openfold_model_ptm_2 openfold_model_no_templ_ptm_1\n",
-        "  do wget -qnc https://files.ipd.uw.edu/krypton/openfold/${W}.npz -P params; done\n",
         "fi"
       ]
     },
@@ -84,14 +82,13 @@
         "model.prep_inputs(get_pdb(\"2MR5\"), chain=\"A\",\n",
         "                  pos=old_pos,               # define positions to contrain\n",
         "                  length=100,                # define if the desired length is different from input PDB\n",
-        "                  fix_seq=False,             # set True to constrain the sequence\n",
-        "                  use_sidechains=False)      # set True to restrain the sidechains\n",
+        "                  fix_seq=False)             # set True to constrain the sequence\n",
         "\n",
         "# set positions (if different from PDB)\n",
         "# reorder the segments, \n",
         "model.rewire(order = [1,2,3,0,7,4,5,6], # set order of segments\n",
         "             loops =  [3,3,3,4,3,3,4],  # change loop length inbetween segments\n",
-        "             offset=0)\n",
+        "             offset=0)                  # essentially loop length at the N term\n",
         "\n",
         "print(model.opt[\"pos\"])"
       ],
@@ -106,12 +103,11 @@
       "source": [
         "# restart optimization\n",
         "model.restart()\n",
+        "# model.set_seq(mode=\"wildtype\") # initialize with wildtype sequence\n",
         "\n",
-        "# balance weights [dgram_cce=restraint weight], [con=hallucination weight]\n",
-        "model.set_weights(dgram_cce=1, con=0.1)\n",
-        "\n",
-        "# design!\n",
-        "model.design_3stage(200,100,10)"
+        "# balance weights [dgram_cce = restraint weight], [con = hallucination weight]\n",
+        "model.set_weights(dgram_cce=1, con=0)\n",
+        "model.design_3stage(300,100,10)"
       ],
       "metadata": {
         "id": "bDA8cPqMT_eY"
@@ -134,7 +130,7 @@
     {
       "cell_type": "code",
       "source": [
-        "HTML(model.animate(dpi=100))"
+        "HTML(model.animate())"
       ],
       "metadata": {
         "id": "9sjG7kvoHaVi"