Differences

This shows you the differences between two versions of the page.

--- secondary_structure_vs_time [2025/10/14 15:20] – admin
+++ secondary_structure_vs_time [2025/11/06 07:20] (current) – [Python Version] edit
@@ Line 1: / Line 1: @@
 **Secondary Structure using STRIDE**
+Update 2025: An alternate version using Python is available at the end of the page - Abhi Senthilkumar
 The code is adopted and changed from the following script for secondary structure calculation in VMD.
@@ Line 27: / Line 29: @@
 {{:sec.jpg?700|}}
+===== Python Version =====
+  - Download {{ :secondary_structure.tar.gz |}} and place it within the directory containing your .dyn files.
+  - Install MDAnalysis, matplotlib, and pandas packages for Python if you haven't already.
+  - Run ''python secondary_structure.py'' to calculate the secondary structure for each timestep in the simulation.
+  - Edit ''plot_secondary_structure.py'' to specify the ''ns_per_dyn''
+  - Run ''python plot_secondary_structure.py'' and the generated graph will be in ''ss.png''
+ {{:ss_python.png?400|}}