How Does Structure Viewer recognize Second Structure Element?

Question

[joey0214.zhong]

How does structure viewer (like RasMol ,PyMOL, etc) recognize the second structure elements(alpha sheet, beta strand,etc)?

Even though in PDB file, it do not have information about which part is alpha sheet or beta strand.

Appreciate any comment and suggestion!

Answer 1

[Jiyao Wang]

Many programs could determine secondary structure based on 3D coordinates. One of the open source programs is DSSP.

iCn3D uses the DSSP program to determine the secondary structure for those PDBs without secondary structure specified. You can use the Node.js script "secondarystructure.js" at https://github.com/ncbi/icn3d/tree/master/icn3dnode to output the PDB with secondary structure specified, or just the secondary structure.

Answer 2

[AsoInfo]

Maybe, this section fulfills your question:

http://www.wwpdb.org/documentation/format23/sect5.html

[joey0214.zhong]

Thanks. But that is the standard PDB file. In a homology predicted structure PDB file, it does not have the information about secondary structure.