How to get list of atomic coordinates and atom names involed in solven accessible area

Question

[iqbal]

Hi folks,

I am not sure if it is relevant place to ask. Could any one tell me if I can can get list of atoms and respective coordinates responsible for solvent accessible surface area?

Thank you very much.

Answer 1

[Jose Manuel Duarte]

You can do it programatically by using Biojava (from version 4). See for instance the tutorial or the demo.

You will be able to do it with either PDB or mmCIF files as input. Thus it will work for even very large molecules. Note that since December 2014 the PDB has transitioned to mmCIF as the main format for data distribution. Legacy programs like NACCESS or AREAIMOL won't be able to read mmCIF files.