Question: 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
gravatar for aditya.k311998
15 months ago by
aditya.k3119980 wrote: this is the link to PDB file I am interested in

biopython python • 405 views
ADD COMMENTlink modified 14 months ago by Biostar ♦♦ 20 • written 15 months ago by aditya.k3119980

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.

ADD REPLYlink written 15 months ago by wojdyr40

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

ADD REPLYlink written 15 months ago by YaGalbi1.4k
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