Docs: RF3 README update and moving RF3 examples

docs/releases/rf3/examples/3en2_from_json_with_msa.json → models/rf3/docs/examples/3en2_from_json_with_msa.json

@@ -4,12 +4,12 @@
         {
             "seq": "AINRLQLVATLVEREV(MSE)RYTPAGVPIVNCLLSYSGQA(MSE)EAQAARQVEFSIEALGAGK(MSE)ASVLDRIAPGTVLECVGFLARKHRSSKALVFHISGLEHHHHHH",
             "chain_id": "A",
-            "msa_path": "docs/rf3/examples/msas/3en2_A.a3m.gz"
+            "msa_path": "models/rf3/docs/examples/msas/3en2_A.a3m.gz"
         },
         {
             "seq": "AINRLQLVATLVEREV(MSE)RYTPAGVPIVNCLLSYSGQA(MSE)EAQAARQVEFSIEALGAGK(MSE)ASVLDRIAPGTVLECVGFLARKHRSSKALVFHISGLEHHHHHH",
             "chain_id": "B",
-            "msa_path": "docs/rf3/examples/msas/3en2_A.a3m.gz"
+            "msa_path": "models/rf3/docs/examples/msas/3en2_A.a3m.gz"
         }
     ]
 }

docs/releases/rf3/examples/7o1r_from_json.json → models/rf3/docs/examples/7o1r_from_json.json

@@ -4,17 +4,17 @@
         "components": [
             {
                 "seq": "MKSLSFSLALGFGSTLVYSAPSPSSGWQAPGPNDVRAPCPMLNTLANHGFLPHDGKGITVNKTIDALGSALNIDANLSTLLFGFAATTNPQPNATFFDLDHLSRHNILEHDASLSRQDSYFGPADVFNEAVFNQTKSFWTGDIIDVQMAANARIVRLLTSNLTNPEYSLSDLGSAFSIGESAAYIGILGDKKSATVPKSWVEYLFENERLPYELGFKRPNDPFTTDDLGDLSTQIINAQHFPQSPGKVEKRGDTRCPYGYH",
-                "msa_path": "docs/rf3/examples/msas/7o1r_A.a3m.gz",
+                "msa_path": "models/rf3/docs/examples/msas/7o1r_A.a3m.gz",
                 "chain_id": "A"
             },
             {
                 "ccd_code": "MG"
             },
             {
-                "path": "docs/rf3/examples/ligands/NAG.cif"
+                "path": "models/rf3/docs/examples/ligands/NAG.cif"
             },
             {
-                "path": "docs/rf3/examples/ligands/HEM.sdf"
+                "path": "models/rf3/docs/examples/ligands/HEM.sdf"
             },
             {
                 "smiles": "[nH]1cc[nH+]c1"

docs/releases/rf3/examples/7xli_template_antigen_and_framework.json → models/rf3/docs/examples/7xli_template_antigen_and_framework.json

@@ -3,10 +3,10 @@
         "name": "7xli_template_antigen",
         "components": [
             {
-                "path": "docs/rf3/examples/templates/7xli_chain_A.cif"
+                "path": "models/rf3/docs/examples/templates/7xli_chain_A.cif"
             },
             {
-                "path": "docs/rf3/examples/templates/7xli_chain_B.cif"
+                "path": "models/rf3/docs/examples/templates/7xli_chain_B.cif"
             }
         ],
         "template_selection": ["A", "B/*/1-42", "B/*/49-63", "B/*/71-102", "B/*/108-125"]

docs/releases/rf3/examples/9dfn_template_ligand_and_protein.json → models/rf3/docs/examples/9dfn_template_ligand_and_protein.json

@@ -3,7 +3,7 @@
         "name": "9dfn_template_ligand_and_protein",
         "components": [
             {
-                "path": "docs/rf3/examples/9dfn.cif"
+                "path": "models/rf3/docs/examples/9dfn.cif"
             }
         ],
         "template_selection": ["A", "C", "D"],

models/rf3/docs/index.md

@@ -8,4 +8,10 @@ to contribute, feel free to open a PR!
 RF3 is an all-atom biomolecular structure prediction network 
 competitive with leading open-source models. By including additional features at train-time – implicit chirality representations and atom-level geometric conditioning – we improve performance on tasks such as prediction of chiral ligands and fixed-backbone or fixed-conformer docking.
 
-For more information, please see our preprint, [Accelerating Biomolecular Modeling with AtomWorks and RF3](https://doi.org/10.1101/2025.08.14.670328).
+**Preprint**: [Accelerating Biomolecular Modeling with AtomWorks and RF3](https://doi.org/10.1101/2025.08.14.670328)
+
+---
+
+For more information on how to run RF3, see the [README](https://github.com/RosettaCommons/foundry/blob/production/models/rf3/README.md).
+
+You can install RF3, and the other models included in [Foundry](https://github.com/RosettaCommons/foundry) by following the instructions in [Foundry's README](https://github.com/RosettaCommons/foundry/blob/production/README.md).