PDB editing using BASH (Linux)
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Entering edit mode
5 months ago

Hi gurus!

I need to do some modifications in a set of 20k PDB files for the same complex (solutions of Brownian dynamics) so that they are suitable for runnig some calculations in a NMR prediction program.

To do that, I'm using BASH. One of the modifications that I need consists of renumbering residues from a certain point (not all of them), because I need two chains with consecutive residue numbering. I'm trying to do it with awk, but I canĀ“t find the way to do it.

Any help?

Thanks in advance!

Renumbering awk BASH PDB • 172 views
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Entering edit mode
5 months ago
Mensur Dlakic ★ 14k

One of the programs I find useful for manipulating PDB files is pdbset, which is a part of the CCP4 package.

For example, to renumber a file 1xyz.pdb so the first residue number is 1, this is all it takes:

pdbset xyzin 1xyz.pdb xyzout 1xyz_renumbered.pdb << EOF
renumber 1
end
EOF

You could easily write a small script that would do this for many files automatically.

A simple Google search turns up bunch of other solutions.

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