formatting arg options as list

OpenFreeEnergy · Oct 9, 2024 · d8192fd · d8192fd
1 parent 912fffb
commit d8192fd
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/showcase/openfe_showcase.ipynb b/showcase/openfe_showcase.ipynb
@@ -1354,13 +1354,14 @@
     " estimates into a single file, use the `openfe gather` command from within the working directory used above:\n",
     "\n",
     "`openfe gather results/ --report dg -o final_results.tsv`\n",
-    "This will write out a tab-separated table of results where the results reported are controlled by the --report option:\n",
     "\n",
-    "`dg` (default) reports the ligand and the results are the maximum likelihood estimate of its absolute free, and the associated uncertainty from DDG replica averages and standard deviations.\n",
+    "This will write out a tab-separated table of results, where the results reported are controlled by the `--report` option:\n",
     "\n",
-    "`ddg` reports pairs of ligand_i and ligand_j, the calculated relative free energy DDG(i->j) = DG(j) - DG(i) and its uncertainty.\n",
+    "* `dg` (default) reports the ligand and the results are the maximum likelihood estimate of its absolute free, and the associated uncertainty from DDG replica averages and standard deviations.\n",
     "\n",
-    "`dg-raw` reports the raw results, giving the leg (vacuum, solvent, or complex), ligand_i, ligand_j, the raw DG(i->j) associated with it."
+    "* `ddg` reports pairs of ligand_i and ligand_j, the calculated relative free energy DDG(i->j) = DG(j) - DG(i) and its uncertainty.\n",
+    "\n",
+    "* `dg-raw` reports the raw results, giving the leg (vacuum, solvent, or complex), ligand_i, ligand_j, the raw DG(i->j) associated with it."
    ]
   },
   {