Klauda Lab Simulation Wiki

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
**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.
[[https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/]]

This analysis computes the secondary structure of protein residues in time for a dcd trajectory. The scripts needed can be downloaded from below.

{{ :secondary_structure.rar |}}

====== Steps ======

  - change the psf and dcd in ss_content.tcl according to where these files are in your directory
  - 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.
  - 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 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.
    

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


{{: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|}}