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
https://files.rcsb.org/view/1CA5.pdb this is the link to PDB file I am interested in
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aditya.k311998 •
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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.
you could also install VMD....load the file....make the selection of what you want to keep.... write a new pdb