[Biojava-l] Fwd: Obtaining second structure with biojava

[Andreas Prlic]

Hi Mohammad,

Please don't send BioJava related questions to me directly, but to the
mailing list.

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.

https://github.com/biojava/biojava-tutorial/blob/master/structure/structure-data-model.md

Hope that helps,

Andreas



---------- Forwarded message ----------
From: Mohammad Taheri <mo.taheri.ledari at gmail.com>
Date: Thu, May 14, 2015 at 2:01 AM
Subject: Obtaining second structure with biojava
To: andreas.prlic at gmail.com


Hello Mr Andreas Prlic.

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
here <https://www.biostars.org/p/107364/> 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.
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.
May you tell me how can i obtain right and exact second structure of a
protein chain by using biojava?

Thank you in advance for your help.
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