[Chimera-users] Mutating to Lysine neutral

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 30 15:49:02 PST 2017

The only difference is the hydrogens, and you can choose to make that lysine neutral when adding hydrogens.  For example, in the AddH dialog (in menu under Tools… Structure Editing), choose “Protonation states for: lysine” and then “Specified individually” to make it ask you the charge state for each lysine.  Or, you could text-edit the PDB file beforehand to change that residue’s name from LYS to LYN and then in this same part of the AddH dialog, choose “Residue-name-based” (which is actually the default setting.  

If you are using the “addh” command there is a similar option “useLysName true” if you edited the residue name to LYN before opening the PDB file in Chimera.

If there are already hydrogens on the structure, you would need to delete them first, e.g. command “delete H”
I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 30, 2017, at 1:00 PM, Alireza Shaneh <ashaneh at gmail.com> wrote:
> Hello,
> I wanted to know if there would be a way to mutate the positively charged Lysine to Lysine neutral in Chimera. 
> Thanks in advance,
> Alireza

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