Hi Elaine, Thank you for the detailed explanation about the protonation states of glutamic acid and lysine in a biological environment. You are absolutely right. I am going to check the suggested options to modify the structure. Thank you. Best regards, Chang On Fri, Nov 15, 2024 at 3:15 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Chang, Normally in the biological environment, most glutamic acid sidechains would not be protonated (it would be "glutamate" with a negative charge, ending in a carboxylate CO2 with no hydrogens on these oxygens). ChimeraX chooses the most likely protonation state in the biological environment, pH near 7.
Although it is possible with several steps to change the glutamic acid sidechain the neutral state, I'm guessing that you are trying to model the most likely state in a biological environment -- In that case, you would actually want a negatively charged glutamate sidechain and you should leave it the way it is.
Similarly, the lysine sidechain will end in -NH3+ meaning that it has a positive charge.
If you want to change these and get the LESS likely protonation state, it is more difficult. One way is to delete all the hydrogens and then change the names of those residues from the standard (e.g. GLU) to the special residue name that means to make it neutral (e.g. GLH) and then use the "addh" command with the corresponding option for that kind of residue, in this example, "useGluName" -- see the help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html>
You could change the residue name by text-editing the input PDB file (outside of ChimeraX, in your favorite text-editing program), or you could use ChimeraX command "setattr" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
However, depending on what you will be using this peptide structure for, like what other programs you will be putting it into, you may need to change back to the standard residue name (e.g. GLU) after adding hydrogens and before saving a PDB file.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2024, at 12:30 PM, Chang Jang via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX users,
I am building a customer peptide containing Glu, Ala, Lys using Build Structure.
Once I built it, I added hydrogens. But, one oxygen in the side chains of Glu does not have a hydrogen added.
How would I fix the structure?
Thanks, Chang