Renumbering Residues in PyMOL

Question

[batillia]

I had a few DNA fragments that I combined into one molecule. However, when PyMOL automatically added the bonds to form the one molecule, some of them appeared incorrect. I'm hoping that renumbering the residues could help this issue but so far I haven't found a decent/working way to do this.

I'm still rather new to this software so any help is appreciated.

Answer 1

[João Rodrigues]

You should renumber them before loading them in Pymol, otherwise you might get overlapping residues and lose information. To do it Pymol, you use the alter command, e.g.,

alter your_selection, resi=int(resi)+1-int(resi)

This would renumber the selection: 1..2..3...etc

Alternatively, to manipulate numberings outside Pymol rather quickly, you can use this set of scripts. pdb_reres.py takes a PDB and a number as input, e.g.,

pdb_reres.py -1 astructure.pdb

This renumbers that structure, sequentially, from 1. Pymol is 'smarter' in the sense that it keeps gaps in the numbering if they exist.