<div dir="ltr">Hi Mohammad,<div><br></div><div>Please don't send BioJava related questions to me directly, but to the mailing list.</div><div><br></div><div>The secondary structure assignment code in BioJava is still in beta. If you want to get the author's assignment of secondary structure (most of the time the same as DSSP assignments), you can take a look at the tutorial for how to access it. Check the section "Working with groups" for an example.</div><div><br></div><div><a href="https://github.com/biojava/biojava-tutorial/blob/master/structure/structure-data-model.md">https://github.com/biojava/biojava-tutorial/blob/master/structure/structure-data-model.md</a><br></div><div><br></div><div>Hope that helps,</div><div><br></div><div>Andreas</div><div><br></div><div><br></div><div><br><div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Mohammad Taheri</b> <span dir="ltr"><<a href="mailto:mo.taheri.ledari@gmail.com">mo.taheri.ledari@gmail.com</a>></span><br>Date: Thu, May 14, 2015 at 2:01 AM<br>Subject: Obtaining second structure with biojava<br>To: <a href="mailto:andreas.prlic@gmail.com">andreas.prlic@gmail.com</a><br><br><br><div dir="ltr">Hello Mr Andreas Prlic.<div><br><div>I am using biojava to load and analyze protein structure, but i have problem with obtaining the secondary structure of a protein. I use the code <a href="https://www.biostars.org/p/107364/" target="_blank">here</a> to get the second structure but it is not giving me right locations of alpha helices. For example it considers some 3/10 helices as alpha helices.</div><div>I even tried using raw pdb file to obtain alpha helices and beta sheets by using toPDB() method of the structure object but this method is not giving me the oroginal pdb file with HELIX and SHEET sections and just giving me atoms section.</div><div>May you tell me how can i obtain right and exact second structure of a protein chain by using biojava?</div><div><br></div><div>Thank you in advance for your help.</div></div></div>
</div><br><br>
</div></div></div>