diff --git a/CHANGELOG.md b/CHANGELOG.md
index c2720191..f510897c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -99,6 +99,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#455](https://github.com/nf-core/proteinfold/issues/455)] - Fix colabfold monomer inheriting id from fasta header.
 - [[#457](https://github.com/nf-core/proteinfold/issues/457)] - Fix colabfold multimer always downloading model weights.
 - [[PR #461](https://github.com/nf-core/proteinfold/pulls/461)] - Update publishdir patterns for HelixFold3 module
+- [[PR #462](https://github.com/nf-core/proteinfold/pulls/462)] - Update publishdir patterns for RoseTTAFold-All-Atom modules
 - [[PR #464](https://github.com/nf-core/proteinfold/pulls/454)] - Update publishdir patterns for Boltz module
 
 ### Parameters
diff --git a/conf/modules_rosettafold_all_atom.config b/conf/modules_rosettafold_all_atom.config
index 63a78c77..ba3c6869 100644
--- a/conf/modules_rosettafold_all_atom.config
+++ b/conf/modules_rosettafold_all_atom.config
@@ -22,11 +22,36 @@ process {
     withName: 'RUN_ROSETTAFOLD_ALL_ATOM' {
         accelerator = params.use_gpu? 1 : 0
         publishDir = [
-                path: { "${params.outdir}/rosettafold_all_atom/" },
+            [
+                path: { "${params.outdir}/rosettafold_all_atom/${meta.id}" },
                 mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                pattern: '*.*'
+                pattern: '*_plddt.tsv'
+            ],
+            [
+                path: { "${params.outdir}/rosettafold_all_atom/${meta.id}" },
+                mode: 'copy',
+                saveAs: { filename -> "paes/$filename" },
+                pattern: '*_[0-5]_pae.tsv'
+            ],
+            [
+                path: { "${params.outdir}/rosettafold_all_atom/${meta.id}" },
+                mode: 'copy',
+                pattern: '*_rosettafold_all_atom_msa.tsv'
+            ],
+            [
+                enabled: params.save_intermediates,
+                path: { "${params.outdir}/rosettafold_all_atom/${meta.id}/raw" },
+                mode: 'copy',
+                pattern: 'raw/**',
+                saveAs: { filename -> filename.toString().replaceFirst(/^raw\//, '') }
+            ],
+            [
+                path: { "${params.outdir}/rosettafold_all_atom/top_ranked_structures" },
+                mode: 'copy',
+                saveAs: { "${meta.id}.pdb" },
+                pattern: '*_rosettafold_all_atom.pdb'
             ]
+        ]
     }
 
     withName: 'NFCORE_PROTEINFOLD:ROSETTAFOLD_ALL_ATOM:MULTIQC' {
diff --git a/modules/local/run_rosettafold_all_atom/main.nf b/modules/local/run_rosettafold_all_atom/main.nf
index 36adcc2a..ef9a217b 100644
--- a/modules/local/run_rosettafold_all_atom/main.nf
+++ b/modules/local/run_rosettafold_all_atom/main.nf
@@ -18,6 +18,7 @@ process RUN_ROSETTAFOLD_ALL_ATOM {
     path (fasta_files)
 
     output:
+    path ("raw/**")                                                     , emit: raw
     tuple val(meta), path ("${meta.id}_rosettafold_all_atom.pdb")       , emit: pdb
     tuple val(meta), path ("${meta.id}_plddt.tsv")                      , emit: multiqc
     tuple val(meta), path ("${meta.id}_rosettafold_all_atom_msa.tsv")   , emit: msa
@@ -55,6 +56,14 @@ process RUN_ROSETTAFOLD_ALL_ATOM {
 
     mv "${meta.id}_msa.tsv" "${meta.id}_rosettafold_all_atom_msa.tsv"
 
+    mkdir -p raw
+    if [[ -d "\$yaml_name" ]]; then
+        mv "\$yaml_name" raw/
+    fi
+    if [[ -f "\${yaml_name}_aux.pt" ]]; then
+        mv "\${yaml_name}_aux.pt" raw/
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python3 --version | sed 's/Python //g')
@@ -65,10 +74,11 @@ process RUN_ROSETTAFOLD_ALL_ATOM {
     """
     touch "${meta.id}_rosettafold_all_atom.pdb"
     touch "${meta.id}.pdb"
-    touch "${meta.id}_aux.pt"
     touch "${meta.id}_plddt.tsv"
     touch "${meta.id}_rosettafold_all_atom_msa.tsv"
     touch "${meta.id}_0_pae.tsv"
+    mkdir -p raw
+    touch raw/${meta.id}_aux.pt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":