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When using Pymol or Coot molecular visualization software to solve x-ray crystallography structures, how can I mutate a cytosine to a 5-methylcytosine?

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  • $\begingroup$ Pymol is a tool for visualization. You cannot modify the molecules with it (how should it know where exactly to place the methyl group? ). You need to modify your molecules source file by hand or with another tool. $\endgroup$
    – danijoo
    May 5, 2015 at 12:59

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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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