JMB-Scripts/Stride-to-Pymol

To assess the secondary structure of your protein with STRIDE in Pymol

Stride to Pymol

This script enables the conversion of STRIDE's secondary structure assignments into a PyMOL-readable format, allowing users to visualize and analyze protein structures with updated secondary structure information

Usage:

1- create the .pml file

python stride-to-pml-vXX.py NameofPdb.pdb

This will produce two files:: 1- Stride.update_ss.pml : PyMOL script to update the protein's secondary structure 2- NameofPdb.stride : STRIDE's output for further analysis.

2- launch pymol

pymol NameofPdb.pdb Stride.update_ss.pml

Requirements:

PyMOL: A molecular visualization system. It can be obtained from the official PyMOL website. (Schrödinger, LLC 2015)

STRIDE: A tool for protein secondary structure assignment from atomic coordinates. Citation: Heinig, M., Frishman, D. (2004). STRIDE: a Web server for secondary structure assignment from known atomic coordinates of proteins. Nucl. Acids Res. , 32, W500-2

Before using the script, ensure that STRIDE and Pymol are installed and accessible from your command line.