Hi Jackie,
If the PDB file has a MODRES record that specifies the "normal" form of the residue, then I believe it will show up as K when you display the sequence. 

For example, if I use these commands

open 7k3m
select :kcx

...and then show its sequence (menu: Favorites... Sequence) I can see that the selected residue is "K" in the sequence.

The PDB file for 7k3m contains this MODRES line:

MODRES 7K3M KCX A   71  LYS  MODIFIED RESIDUE

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

> On Feb 23, 2022, at 11:39 PM, Jacqueline Vitali <jackie.vitali@gmail.com> wrote:
>
> I have a "residue" KCX (PDB records are Hetatm).  In the sequence alignment it comes as X.  Is there a way to change it to K without making a PDB file and changing it to K there?  Thank you,.
>
> Jackie Vitali
> Cleveland State University