Renumber

Type	Python Module
Download	renumber.py
Author(s)	Thomas Holder
License	BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

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)

See Also

• alter
• rename
• pdb_retain_ids