Renumber
renumber sets new residue numbers (resi) for a polymer based on connectivity.
Example
This examples takes a pdb structure with insertion codes and sets a new, linear numbering based on Q8N2U3_HUMAN.
fetch 1h4w, async=0 # move everything which is not polymer to another chain alter not polymer, chain="B" # renumber polymer, first 27 residues of Q8N2U3_HUMAN missing. renumber chain A, 28
This example fixes numbering after concatenating two chains with fuse. Note that the cartoon representation and the sequence viewer need sorting to display correctly.
fab ACDEFG, chain1 fab HIKLMN, chain2 disable chain1 as cartoon fuse last (chain1 and name C), first (chain2 and name N) renumber chain2 sort chain2
Troubleshooting
For large molecules it might be necessary to increase the python recursion limit:
import sys sys.setrecursionlimit(10**5)