Help To Separate Subsections Of Pdb File

Question

[snlpatel001213]

i m working on making a programme, in that i need to separate ligand and receptor coordinate from pdb file via c programe , but i m unable to find a specific demarcation between coordinates of above two in file please help

[Pappu]

grep ^ATOM *.pdb grep ^HETATM *.pdb Should do the job.

Answer 1

[wdiwdi]

Well, if you are lucky, you just need to distinguish between ATOM and HETATM lines, and then throw out water, metal ions, etc. This however only works if you have a cleanly tagged PDB file - many are not, and you can code an open-ended amount of additional program intelligence in sorting out the role of an atom from its context if all are just ATOMs.

I wonder why you need to write a new program, though. There are plenty of PDB handler applications available which already do what you need.