When using Pymol or Coot molecular visualization software to solve x-ray crystallography structures, how can I mutate a cytosine to a 5-methylcytosine?
I got the answer on a Pymol listserve:
Yes, it can be done in Pymol.
Choose the residue you want to mutate from cytosine to 5-methylcytosine. Use Action - Hydrogens - Add function to add hydrogens. Change mouse selection to choose atoms.
Click on the hydrogen you want to replace.
Click builder (there is more work to do if you're on a Mac, see below) to open builder window.
If you're on a Mac, you won't have Builder functionality unless you change your MacPyMOL.app file name to PyMOLX11Hybrid.app