ShiftRes for 1-407 only?

PDB-tools
1

6ef8 has 7 chains, protein numbered 1-407, plus hetero atoms HEC (heme). I would like to shift the protein residue numbers +25 without shifting the hetero numbering. Ideally I would like chain A only, with protein shifted +25 and keeping hetero not shifted. How?

I thought I could use pdb_selres but I cannot guess the syntax to specify a number range for the web server. I want to select 1 to 407 (which would exclude hetero). I tried “1:407:1”, or “1 407 1” for start, stop, step, but when I click “run” I get nothing, or an obscure error message. “1,407,1” selects only residues 1 and 407.

Am I correct in thinking that I will need to shiftres the protein, then manually cut and paste the hetero atom lines onto the shiftres output?

2

Seems to be like a simple solution indeed.

3

Hi @ericmartz

Sorry for the late reply. It is actually possible to solve that more complex issue with the pdb-tools command line. That’s how I solved your case, to what I understood were your needs:

# first download the pdb
pdb_fetch 6ef8 > 6ef8.pdb

# select the chaina to a different file with residues renumbered
pdb_keepcoord 6ef8.pdb | pdb_selchain -A | pdb_reres -25 | pdb_delhetatm > chaina.pdb

# select only the het atoms
pdb_keepcoord 6ef8.pdb | pdb_selchain -A | pdb_selhetatm > het.pdb

# merge both chaina.pdb and het.pdb
pdb_merge chaina.pdb het.pdb | pdb_tidy > final.pdb

You can find all information about the pdb-tools command line here: pdb-tools | A swiss army knife for editing PDB files.

This should get you what you need.
Best,