# ShiftRes for 1-407 only?

**URL:** <https://ask.bioexcel.eu/t/shiftres-for-1-407-only/2872>\
**Category:** PDB-tools\
**Created:** [March 27, 2021, 11:07pm UTC](https://ask.bioexcel.eu/t/shiftres-for-1-407-only/2872 "2021-03-27T23:07:08Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ericmartz](https://avatars.discourse-cdn.com/v4/letter/e/73ab20/32.png) [@ericmartz](https://ask.bioexcel.eu/u/ericmartz)\
**Post date:** [March 27, 2021, 11:07pm UTC](https://ask.bioexcel.eu/t/shiftres-for-1-407-only/2872/1 "2021-03-27T23:07:08Z")

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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?

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [March 29, 2021, 6:53am UTC](https://ask.bioexcel.eu/t/shiftres-for-1-407-only/2872/2 "2021-03-29T06:53:20Z")

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Seems to be like a simple solution indeed.

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**Author:** ![joaomcteixeira](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaomcteixeira/32/480_2.png) [@joaomcteixeira](https://ask.bioexcel.eu/u/joaomcteixeira)\
**Post date:** [September 15, 2021, 8:51am UTC](https://ask.bioexcel.eu/t/shiftres-for-1-407-only/2872/3 "2021-09-15T08:51:47Z")

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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:

```auto
# 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.](http://www.bonvinlab.org/pdb-tools/)

This should get you what you need.  
Best,