Modified DNA bases in Pymol and Coot

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.


Click C


If you're on a Mac, you won't have Builder functionality unless you change your MacPyMOL.app file name to PyMOLX11Hybrid.app


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