Differences

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

--- secondary_structure_vs_time [2021/11/07 19:37] – [Steps] edit
+++ secondary_structure_vs_time [2021/11/07 19:53] (current) – [Steps] edit
@@ Line 15: / Line 15: @@
   - 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
+   for i in {1..40};do
+     sed '1~10!d' sec_structure-$i.dat >> ss_content.dat
+   done
+the line sed '1~10!d' in above means, we are only taking every 10th line of the secondary structure vs time.
-sed '1~10!d' sec_structure-$i.dat >> ss_content.dat
+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
-done
+{{:sec.jpg?700|}}