As an example,you can find here the links of the structure **5PTI** to its

[PDB file](http://www.rcsb.org/pdb/files/5PTI.pdb) (search for the HELIX and SHEET lines) and its

[DSSP file](http://www.rcsb.org/pdb/files/5PTI.dssp).

String pdbID = "5pti";

//Only change needed to the normal Structure loading

params.setParseSecStruc(true); //this is false as DEFAULT

//The loaded Structure contains the SS assigned

Structure s = cache.getStructure(pdbID);

//If the more detailed DSSP prediction is required call this afterwards

DSSPParser.fetch(pdbID, s, true); //Second parameter true overrides the previous SS

For more examples search in the **demo** package for `DemoLoadSecStruc`.

A brief explanation of the algorithm and the output format can be found

[here](http://swift.cmbi.ru.nl/gv/dssp/DSSP_3.html).

The interface is very easy: a single method, named *predict()*, calculates the SS and can assign it to the

input Structure overriding any previous annotation, like in the DSSPParser. An example can be found below:

String pdbID = "5pti";

AtomCache cache = new AtomCache();

//Load structure without any SS assignment

Structure s = cache.getStructure(pdbID);

//Predict and assign the SS of the Structure

SecStrucPred ssp = new SecStrucPred(); //Instantiation needed

ssp.predict(s, true); //true assigns the SS to the Structure

BioJava Class: [org.biojava.nbio.structure.secstruc.SecStrucPred]

(http://www.biojava.org/docs/api/org/biojava/nbio/structure/secstruc/SecStrucPred.html)

Because there are different sources of SS annotation, the Sata Structure in **BioJava** that stores SS assignments

has two levels. The top level `SecStrucInfo` is very general and only contains two properties: **assignment**

(String describing the source of information) and **type** the SS type.

However, there is an extended container `SecStrucState`, which is a subclass of `SecStrucInfo`, that stores

all the information of the hydrogen bonding, turns, bends, etc. used for the SS prediction and present in the

DSSP output file format. This information is only used in certain applications, and that is the reason for the

more general `SecStrucInfo` class being used by default.

In order to access the SS information of a `Structure`, the `SecStrucInfo` object needs to be obtained from the

`Group` properties. Below you find an example of how to access and print residue by residue the SS information of

a `Structure`:

//This structure should have SS assigned (by any of the methods described)

Structure s;

for (Chain c : s.getChains()) {

for (Group g: c.getAtomGroups()){

if (g.hasAminoAtoms()){ //Only AA store SS

//Obtain the object that stores the SS

SecStrucInfo ss = (SecStrucInfo) g.getProperty(Group.SEC_STRUC);

//Print information: chain+resn+name+SS

System.out.println(c.getChainID()+" "+

g.getResidueNumber()+" "+

g.getPDBName()+" -> "+ss);

}

}

}

Once the SS has been assigned (either loaded or predicted), there exist in **BioJava** some formats to visualize it:

- **DSSP format**: the SS can be printed as a DSSP oputput file format, following the standards so that it can be

parsed again. It is the safest way to serialize a SS annotation and recover it later, but it is probably the most

complicated to visualize.

<pre>

# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA

1 1 A R 0 0 168 0, 0.0 54,-0.1 0, 0.0 5,-0.1 0.000 360.0 360.0 360.0 139.2 32.2 14.7 -11.8

2 2 A P > - 0 0 45 0, 0.0 3,-1.8 0, 0.0 4,-0.3 -0.194 360.0-122.0 -61.4 144.9 34.9 13.6 -9.4

3 3 A D G > S+ 0 0 122 1,-0.3 3,-1.6 2,-0.2 4,-0.2 0.790 108.3 71.4 -62.8 -28.5 35.8 10.0 -9.5

4 4 A F G > S+ 0 0 26 1,-0.3 3,-1.7 2,-0.2 -1,-0.3 0.725 83.7 70.4 -64.1 -23.3 35.0 9.7 -5.9

</pre>

- **FASTA format**: simple format that prints the SS type of each residue sequentially in the order of the aminoacids.

It is the easiest to visualize, but the less informative of all.

<pre>

>5PTI_SS-annotation

GGGGS S EEEEEEETTTTEEEEEEE SSS SS BSSHHHHHHHH

</pre>

- **Helix Summary**: similar to the FASTA format, but contain also information about the helical turns.

<pre>

3 turn: >>><<<

4 turn: >444< >>>>XX<<<<

5 turn: >5555<

SS: GGGGS S EEEEEEETTTTEEEEEEE SSS SS BSSHHHHHHHH

AA: RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA

</pre>

- **Secondary Structure Elements**: another way to visualize the SS annotation is by compacting those sequential residues that share the same SS type and assigning an ID to the range. In this way, a structure can be described by

a collection of helices, strands, turns, etc. and each one of the elements can be identified by an ID (i.e. helix 1 (H1), beta-strand 6 (E6), etc).

<pre>

G1: 3 - 6

S1: 7 - 7

S2: 13 - 13

E1: 18 - 24

T1: 25 - 28

E2: 29 - 35

S3: 37 - 39

S4: 42 - 43

B1: 45 - 45

S5: 46 - 47

H1: 48 - 55

</pre>

You can find examples of how to get the different file formats in the class `DemoSecStrucPred` in the **demo**

package.