<img src="docs/Images/Github_readme.png" height="125"/>
### The Project
This project combines different tools for modeling and simulation of RNA structures.
Furthermore, functionalities were developed to efficiently analyze MD trajectories of
labeled RNA. Here, the simulation of FRET experiments plays an essential role.
Using the pipeline described here, RNA structures can be modeled and evaluated using
smFRET experimental data.
## Installation
You can set up **FAMP** in two different ways, depending on how much control you want over the environment:
1. **Manual installation**
- Maximum freedom to choose your own versions of ViennaRNA, Rosetta, GROMACS and other tools/drivers.
- Be aware: leaving out certain dependencies may limit functionality.
2. **Build your own Docker image from our Dockerfile instructions with and without GPU support**
- Requires building the Docker Container, but keeps setup reproducible.
---
### Get the source code
You can download the source via the green **“Code”** button above or clone it directly from the terminal:
```bash
git clone https://github.com/BoernerLab/FAMP_rna.git
```
### Requirements
As a dependency of this notebook the following programms should be preinstalled. Please follow the installation instructions of the tools.
[**ViennaRNAPackge**](https://www.tbi.univie.ac.at/RNA/documentation.html#install)
[**Rosetta**](https://new.rosettacommons.org/docs/latest/build_documentation/Build-Documentation)
[**GROMACS**](https://manual.gromacs.org/documentation/2021.2/install-guide/index.html)
Make sure that the programms are added to the bashrc or zshrc file.
Please create an anaconda environment for this Jupyter Notebook by importing the environment.yml file.
Before you start open Pymol in your environment and install the plugins FRETraj and FRETlabel. Locate the
package with `fretlabel --path` and remember this path. Then open PymMol and go to Plugin -> Plugin manager -> Install
New Plugin -> Choose file ... -> and select fretlabel_gui.py, wich can be found at the path from the step bevore. The
same works for the FRETraj GUI.
### Author
Felix Erichson | erichson(at)hs-mittweida.de
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