I want to extract all Nitrogen of amino acid LYS and O5' Oxygen of DNA which are less than 5 angstrom apart by using Biopython from pdb file 1ca5

Question

[aditya.k311998]

https://files.rcsb.org/view/1CA5.pdb this is the link to PDB file I am interested in

[wojdyr]

If you only want to find pair of atoms that are explicitly listed in the file (i.e. if you want to ignore symmetry operators -- a LYS residue could be far from a particular O5' atom in the same asu, but close to its symmetric image) then it's simple. But in general, if you want to account for crystal symmetry, I don't think that Biopython can help.

[BioinfGuru]

you could also install VMD....load the file....make the selection of what you want to keep.... write a new pdb