Update README.md

README.md

@@ -1,2 +1,16 @@
 # stride_consensus
-stride_consensus
+This python script takes as single argument an output file generated by the secondary structure assignment program STRIDE ([PMID 15215436](https://pubmed.ncbi.nlm.nih.gov/15215436/) ; https://webclu.bio.wzw.tum.de/stride), compares the secondary structure assignments for multiple copies of the same protein and generates a combined sequence and average secondary structure profile.
+
+If the starting set of coordinates contains information for different proteins, the corresponding ATOM lines should be separated into multiple files before running STRIDE and then analyzing its output with stride_consensus.
+
+The secondary structure codes (SSCs) output by the program match those of STRIDE:
+
+<b>H</b> = Alpha helix  
+<b>G</b> = 3-10 helix  
+<b>I</b> = PI-helix  
+<b>E</b> = Extended conformation  
+<b>B</b> (or b) = Isolated bridge  
+<b>T</b> = Turn  
+<b>C</b> = Coil  
+
+In addition, the consensus secondary structure profile generated by the program will contain <b>S</b> or <b>l</b> (lowercase L) SSCs for residues whose assignments are tied between H, G, I, E or B, T, C, respectively.