Hi Prathvi,

"before extracting" doesn't really make sense, but yes, you can do it in multiple steps:

(1) delete all the atoms you don't want, i.e. everything except the serine and the carbonyl of the residue before the serine.

For example, you could select the atoms you want to keep, then invert selection, then delete selection.  There are lots of other ways, just use whichever you think is the easiest.

(2) build the other oxygen onto the carbonyl with Build Structure (in menu under Tools... Structure Editing), Modify Structure section.  That itself takes multiple steps, you would need to change the carbonyl carbon to "trigonal with 3 bonds" (keeping element C), which will put a H where you want the OH,  and then you have to change that H to "O with 1 bond".

You can do all this with either Chimera or ChimeraX.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 3, 2024, at 9:28 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hi Elaine,
>
> I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting?
>
> Thanks in advance,
> Prathvi Singh,
> Research Fellow,
> Department of Biological Sciences & Bioengineering,
> Indian Institute of Technology, Kanpur-208016