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--- secondary_structure_vs_time [2021/11/07 19:36] – [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 10: / Line 12: @@
 ====== Steps ======
-  - 1) change the psf and dcd in ss_content.tcl according to where these files are in your directory
+  - change the psf and dcd in ss_content.tcl according to where these files are in your directory
-  - 2) change the last_file number in ss_content.csh according to the number of trajectories. If you are using a supercomputer other than deepthought2 change this file accordingly.
+  - change the last_file number in ss_content.csh according to the number of trajectories. If you are using a supercomputer other than deepthought2 change this file accordingly.
-  - 3) run ss_content.csh ( sbatch ss_content.csh)
+  - run ss_content.csh ( sbatch ss_content.csh)
-) this will give you multiple .dat files containing the secondary structure in each trajectory. you can combine these into a single secondary_structure file for further analysis.
+  - this will give you multiple .dat files containing the secondary structure in each trajectory. you can combine these into a single secondary_structure file for further analysis.This can be done by the following code:
-This can be done by the following code:
+   for i in {1..40};do
+     sed '1~10!d' sec_structure-$i.dat >> ss_content.dat
+   done
+the line sed '1~10!d' in above means, we are only taking every 10th line of the secondary structure vs time.
-for i in {1..40};do
+To visualize the secondary structure you can use the Matlab file ss_content.m you need to change a few things in this file:  num_residues, num_timesteps, step-size,  and residue names at the end. You can run this file locally on you pc/mac or on the cluster
-sed '1~10!d' sec_structure-$i.dat >> ss_content.dat
-done
+{{: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|}}