I am working with a structure that is largely a protein, and there is a short oligonucleotide associated with it. In the tools  menu the sequence of the protein is Chain A and the short oligonucleotide is Chain C. I have shown their respective sequences. I also know how to highlight components of each chain etc.

However, there is a short dinucleotide with two thymine residues that are also part of the structure. I was able to select these residues and the two thymine residues in the oligonucleotide by using the SELECT menu: residues: dT. So in total four thymine residues are selected and with the ACTIONS menu I can visualize them. Going to Chain C I can hide the two thymine residues on the longer oligo.

How can I select the other two thymine residues that make up the short dinucleotide?

One of these thymines is covalently bound to a tyrosine residue through a phosphodiester bond. I can visualize the tyrosine monophosphate through Chain A, and one can see it  connected to the relevant thymine residue.

But I  would like to color the two thymine residues. But I cannot select them or at least I do not know how to select them.

I am not an expert at using the command line. Likely there is something there.

Again your assistance is sincerely appreciated.

Arthur G. Szabo