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--- secondary_structure_vs_time [2021/11/07 19:52] – [Steps] edit
+++ secondary_structure_vs_time [2025/11/06 07:20] (current) – [Python Version] edit
@@ Line 1: / Line 1: @@
-**Secondary Structure using DSSP**
+**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 25: / Line 27: @@
-{{:sec.jpg?200|}}
+{{: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|}}