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
0
gravatar for aditya.k311998
15 months ago by
aditya.k3119980 wrote:

https://files.rcsb.org/view/1CA5.pdb 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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1641 users visited in the last hour