From 14ebe5fa80a8b25face08472df287e91adae6e37 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 7 Sep 2026 15:07:26 +0100
Subject: [PATCH 1/2] chore: corrected logo file path locations and include
 example usage demo

---
 README.md | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 4a81c76..949dd5f 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,5 @@
-<p align="center" width="100%">
-  <img src="https://raw.githubusercontent.com/CCPBioSim/branding/refs/heads/main/logos/prepmd/prepmd-logo-black-text.svg" width="256px" >
-</div>
-
+prepmd
+==============================
 
 | Category       | Badges |
 |----------------|--------|
@@ -11,14 +9,16 @@
 | **Anaconda**       | [![Anaconda.org](https://anaconda.org/CCPBioSim/prepmd/badges/version.svg)](https://anaconda.org/CCPBioSim/prepmd/) [![Last Updated](https://anaconda.org/CCPBioSim/prepmd/badges/latest_release_date.svg)](https://anaconda.org/CCPBioSim/prepmd) [![Platforms](https://anaconda.org/CCPBioSim/prepmd/badges/platforms.svg)](https://anaconda.org/CCPBioSim/prepmd) [![License](https://anaconda.org/CCPBioSim/prepmd/badges/license.svg)](https://anaconda.org/CCPBioSim/prepmd) [![Downloads](https://anaconda.org/CCPBioSim/prepmd/badges/downloads.svg)](https://anaconda.org/CCPBioSim/prepmd)|
 | **Quality**    | [![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/prepmd/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/prepmd?branch=main) |
 
-A utility to automatically prepare structures from the PDB for molecular dynamics simulation and perform minimisations and simple MD simulations.
 
-## Example usage
 <p align="center">
-    <img src="docs/_static/logos/prepmd-logo-white-text.svg#gh-dark-mode-only" alt="prepmd logo" width="300"/>
-    <img src="docs/_static/logos/prepmd-logo-black-text.svg#gh-light-mode-only" alt="prepmd logo" width="300"/>
+    <img src="docs/source/_static/logos/prepmd-logo-white-text.svg#gh-dark-mode-only" alt="prepmd logo" width="300"/>
+    <img src="docs/source/_static/logos/prepmd-logo-black-text.svg#gh-light-mode-only" alt="prepmd logo" width="300"/>
 </p>
 
+A utility to automatically prepare structures from the PDB for molecular dynamics simulation and perform minimisations and simple MD simulations.
+
+## Example usage
+<img width="768" height="432" alt="demo" src="https://github.com/user-attachments/assets/f7785a4d-ef54-428d-b193-1cb6413bc21e" />
 
 ## Features
 * Automatically download structures, sequences and metadata from the PDB, PDB-REDO, EMDB and UNIPROT

From 51c65ae06870c6361ad6bae5b930a7827069535f Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 7 Sep 2026 15:09:42 +0100
Subject: [PATCH 2/2] chore: reorder paragraph placement within `README.md`

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 949dd5f..d86aec6 100644
--- a/README.md
+++ b/README.md
@@ -9,13 +9,13 @@ prepmd
 | **Anaconda**       | [![Anaconda.org](https://anaconda.org/CCPBioSim/prepmd/badges/version.svg)](https://anaconda.org/CCPBioSim/prepmd/) [![Last Updated](https://anaconda.org/CCPBioSim/prepmd/badges/latest_release_date.svg)](https://anaconda.org/CCPBioSim/prepmd) [![Platforms](https://anaconda.org/CCPBioSim/prepmd/badges/platforms.svg)](https://anaconda.org/CCPBioSim/prepmd) [![License](https://anaconda.org/CCPBioSim/prepmd/badges/license.svg)](https://anaconda.org/CCPBioSim/prepmd) [![Downloads](https://anaconda.org/CCPBioSim/prepmd/badges/downloads.svg)](https://anaconda.org/CCPBioSim/prepmd)|
 | **Quality**    | [![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/prepmd/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/prepmd?branch=main) |
 
+A utility to automatically prepare structures from the PDB for molecular dynamics simulation and perform minimisations and simple MD simulations.
 
 <p align="center">
     <img src="docs/source/_static/logos/prepmd-logo-white-text.svg#gh-dark-mode-only" alt="prepmd logo" width="300"/>
     <img src="docs/source/_static/logos/prepmd-logo-black-text.svg#gh-light-mode-only" alt="prepmd logo" width="300"/>
 </p>
 
-A utility to automatically prepare structures from the PDB for molecular dynamics simulation and perform minimisations and simple MD simulations.
 
 ## Example usage
 <img width="768" height="432" alt="demo" src="https://github.com/user-attachments/assets/f7785a4d-ef54-428d-b193-1cb6413bc21e" />