RosettaCommons · rclune · May 30, 2026 · Jun 2, 2026 · Jun 3, 2026 · Jun 3, 2026
diff --git a/models/rfd3/docs/.assets/binder_tutorial/8aom_choosing_hotspots.png b/models/rfd3/docs/.assets/binder_tutorial/8aom_choosing_hotspots.png
diff --git a/models/rfd3/docs/.assets/binder_tutorial/8aom_cleaned_structure.png b/models/rfd3/docs/.assets/binder_tutorial/8aom_cleaned_structure.png
diff --git a/models/rfd3/docs/.assets/binder_tutorial/8aom_crop_selection.png b/models/rfd3/docs/.assets/binder_tutorial/8aom_crop_selection.png
diff --git a/models/rfd3/docs/.assets/binder_tutorial/8aom_initial_structure.png b/models/rfd3/docs/.assets/binder_tutorial/8aom_initial_structure.png
diff --git a/models/rfd3/docs/.assets/binder_tutorial/8aom_pld1_only.png b/models/rfd3/docs/.assets/binder_tutorial/8aom_pld1_only.png
diff --git a/models/rfd3/docs/.assets/binder_tutorial/cd28_cleaned.png b/models/rfd3/docs/.assets/binder_tutorial/cd28_cleaned.png
diff --git a/models/rfd3/docs/.assets/binder_tutorial/cd28_hotspots.png b/models/rfd3/docs/.assets/binder_tutorial/cd28_hotspots.png
diff --git a/models/rfd3/docs/.assets/binder_tutorial/pdf1_bb1_hotspots.png b/models/rfd3/docs/.assets/binder_tutorial/pdf1_bb1_hotspots.png
diff --git a/models/rfd3/docs/.assets/binder_tutorial/pld1_hotspot_atom_label.png b/models/rfd3/docs/.assets/binder_tutorial/pld1_hotspot_atom_label.png
diff --git a/models/rfd3/docs/.assets/pdf1_hotspots.png b/models/rfd3/docs/.assets/pdf1_hotspots.png
diff --git a/models/rfd3/docs/examples/na_binder_design.md b/models/rfd3/docs/examples/na_binder_design.md
@@ -85,7 +85,7 @@ Example on RNA. Similar to the ssDNA example, example 2.
 
 ### 5. Complex example based on a protein-dsDNA input pdb with parts of protein and dna partially fixed (indexed and unindexed), with Hbond conditioning
 
-This is a complex example which has a dsDNA specified in the contig: `C5-18` and `D24-37`. However, it also specifies an indexed protein motif component (`A146-154`) and diffuses the two flanks of the protein indexed region in the same chain. The diffused protein region has an unindexed motif specified via `"unindex": "/0,/0,B251-B255".` (*Note: the chain breaks applied are analogous to the contig string*). Parts of the DNA have been specified as fixed or to be sampled by RFD3 (`select_fixed_atoms`). Additionally hydrogen bond conditioning is applied to some backbone and base atoms of a few DNA bases.
+This is a complex example which has a dsDNA specified in the contig: `C5-18` and `D24-37`. However, it also specifies an indexed protein motif component (`A146-154`) and diffuses the two flanks of the protein indexed region in the same chain. The diffused protein region has an unindexed motif specified via `"unindex": "/0,/0,B251-255".` (*Note: the chain breaks applied are analogous to the contig string*). Parts of the DNA have been specified as fixed or to be sampled by RFD3 (`select_fixed_atoms`). Additionally hydrogen bond conditioning is applied to some backbone and base atoms of a few DNA bases.
 
 To run this without warnings, you will need to install [hbplus](https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/) to enable hydrogen bond metrics computation. This is discussed at the end of the RFD3 README, but the instructions are reproduced here for convenience:
 

diff --git a/models/rfd3/docs/index.rst b/models/rfd3/docs/index.rst
@@ -38,6 +38,7 @@ RFD3, we recommend starting with the introductory tutorials before moving on to
    :maxdepth: 1
 
    tutorials/intermediate_enzyme_design_tutorial.md
+   tutorials/binder_design_tutorial.md
 
 Examples
 --------

diff --git a/models/rfd3/docs/tutorials/binder_design_tutorial.md b/models/rfd3/docs/tutorials/binder_design_tutorial.md
diff --git a/models/rfd3/docs/tutorials/binder_design_tutorial_files/8AOM.pdb b/models/rfd3/docs/tutorials/binder_design_tutorial_files/8AOM.pdb