Update README.md

README.md

@@ -27,7 +27,7 @@ This model strikes a balance between reconstruction fidelity and structural loca
 
 - Encoding Structures into Tokens (See [genbio-ai/AIDO.StructureEncoder](https://huggingface.co/genbio-ai/AIDO.StructureEncoder))
 - Decoding Tokens into Structures (See [genbio-ai/AIDO.StructureDecoder](https://huggingface.co/genbio-ai/AIDO.StructureDecoder))
-- Reconstructing Structures (See [below](#reconstructing-structures))
+- Reconstructing Structures (See [below](#how-to-use))
 - Structure Prediction (See [this section](https://huggingface.co/genbio-ai/AIDO.Protein2StructureToken-16B/blob/main/README.md#structure-prediction) in genbio-ai/AIDO.Protein2StructureToken-16B)
 
 ## Results
@@ -42,12 +42,10 @@ This model strikes a balance between reconstruction fidelity and structural loca
 ## How to Use
 Please see `experiments/AIDO.StructureTokenizer` in [Model Generator](https://github.com/genbio-ai/modelgenerator) for more details.
 
-### Reconstructing Structures
-
-#### Setup
+### Setup
 Install [Model Generator](https://github.com/genbio-ai/modelgenerator)
 
-#### Data preparation
+### Data preparation
 
 To reproduce the reconstruction results in the paper, we provide a preprocessed CASP15 dataset at [genbio-ai/sample-structure-dataset](https://huggingface.co/datasets/genbio-ai/sample-structure-dataset). It could be downloaded via
 ```bash
@@ -75,7 +73,7 @@ python experiments/AIDO.StructureTokenizer/register_dataset.py \
 
 You need to replace the `folder_path` and the `registry_path` in the following steps accordingly.
 
-#### Running Encoding and Decoding Task
+### Running Encoding and Decoding Task
 
 If you use the provided CASP15 dataset, you can run the combined encoding and decoding task using the following command:
 ```bash
@@ -107,7 +105,7 @@ The input and the output can be summarized as follows:
 - Currently, this function only supports single GPU inference due to the file saving mechanism. We plan to support multi-GPU inference in the future.
 - The reconstructed structures are aligned to the original structures using the Kabsch algorithm. This makes it easier to visualize and compare the structures.
 
-#### Visualizing the Reconstructed Structures
+### Visualizing the Reconstructed Structures
 
 We use VS Code + [Protein Viewer Extension](https://marketplace.visualstudio.com/items?itemName=ArianJamasb.protein-viewer) to visualize the protein structures. It's a beginner-friendly tool for VS Code users. You could also use your preferred protein structure viewer to visualize the structures (e.g., PyMOL, ChimeraX, etc.), but here we focus on this extension.