Hi Shirin,

You can not add hetam in phenix. You have to do it while building your model in coot.

From the right toolbar in the coot, you'll find an option to be used for adding water and ions (probably the + sign).

Choose other and enter Mg then click ok.

This will place a Mg2+ in that blob of yours. Save it and refine it.

Do the whole thing while your pointer in your coot is placed in the middle of the blob where you want to put Mg.

Happy modelling !

Best,

Abhisek

On Mon, Jul 6, 2020 at 4:16 PM Shirin Akbar <shirin.akbar09@gmail.com> wrote:

Dear all,

I am using the phenix.real_space_refine program for refinement of crystal structure in cryo-EM map (ribosome map, 3.4 A resolution). Prior to real_space_refinement I had removed all the heteroatoms. What is the correct way to add the cations (eg. Mg2+ ions) to the structure and how do I do it? Can anyone kindly suggest..

Thanks & Regards
Shirin

--
Shirin Akbar

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Abhisek Mondal, Ph.D.

Cardiovascular Research Institute
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Abhisek Mondal, Ph.D.
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