Run SA2py

Setup your environnement

Clone the repository 

git clone https://github.com/ElouanBethuel/SASA.git

Move to the project directory 

cd SASA

Install conda
Install mamba 

conda install mamba -n base -c conda-forge

Create and activate the conda environnement 

conda env create -f sasa_project.yml
conda activate sasa_project


Run the program

Run with the program : 

python main.py 7kh5 100

Execute the script main.py with the pdf file 7kh5.pdb and with 100 points to model the solvation sphere.
You can replace 7kh5 by any another PDB ID. This program work with many PDB files.If the PDB file format is not compatible an error message is raise.

To create also graphics and pymol files for visualisation add the argument -s

python main.py 7kh5 100 -s


Outputs

IIn the shell, the Solvent Accessible Surface Area of the protein is displayed :

Calculates the solvent accessible surface area from the 7kh5 PDB file :

Downloading the PDB file    
Loading the PDB file

Downloading PDB structure '7kh5'...


Calculation ongoing, please wait a few seconds...

=================
Final result :  
The solvent accessible surface area of the protein : 6503.51 Ų

Files generated

With by default arguments : - The pdb file - A text file with the solvent accessibility of each atom


With additional arguments (-s) : - A png file (graph) to visualize the points created around a atom - A png file (graph) showing solvent accessibility by atom category - A png file (graph) showing solvent accessibility by amino acid category - A pymol file for showing the accessibility of the protein surface - A pymol file for showing the neighbors selection

This files are stored in two folders

  • Outputs : for stored all outputs
  • PDB : for stored all pdb files

The file name format is always the same (exemple with the 7kh5 pdb ID)

  • pdb file : pdb7kh5.ent (pdb + pdb_id + .ent)
  • png file : pdb_id + name_file + .png
  • texte file : pdb_id + .txt
  • pymol file (neihgbors) : pdb_id + _neighbors.pse
  • pymol file (surface) : pdb_id + _surface.pse

To visualize pymol files with the shell

pymol outputs/7kh5_surface.pse

image

This image shows the 7kh5 protein with its surface coloured according to its accessibility to the solvent: the blue parts are the least accessible and the red ones the most accessible.