Chimera learns that non-standard residues are modified forms of regular amino/nucleic acids from the MODRES records in PDB files. If you added MODRES records for your residues to your input file, the sequence would show S/T instead of X. The format for a MODRES record is documented here:

You could crib MODRES records for your residues from 1vrv (SEP) and 6ar2 (TPO). You would have to edit the chain ID and sequence number fields of those records.

—Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Feb 5, 2020, at 7:34 AM, Daniel Hilger <daniel.hilger@pharmazie.uni-marburg.de> wrote:

Hi,

I modeled two phosphorylated residues in my structure. The primary sequence window in Chimera, however, is only showing a “X” at those positions. Is there a possibility to change that to the original amino acid (S or T) or to show them as SEP or TPO in the sequence window?
Thanks,
Daniel

Daniel Hilger, Dr.
Group leader
Philipps-University Marburg
Marbacher Weg 6
35032 Marburg
Germany
daniel.hilger@pharmazie.uni-marburg.de
Phone: +49 6421 28 25930

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