[phenixbb] Magnesium or calcium

Nathaniel Echols nechols at lbl.gov
Sat Mar 2 14:57:11 PST 2013

On Sat, Mar 2, 2013 at 10:21 AM, Daniel Slade <DSlade at scripps.edu> wrote:
> So the resolution is 1.6 and I remember the B factor for mg at 16. I haven't
> checked the coordinating residues. It coordinates acidic residues, a
> backbone carbonyl and one water. I'm now leaning towards calcium as the
> other calciums have bonds distances similar to this one, but not nearly as
> high an affinity.

I guess now is a good time to mention a new (experimental) feature: if
you download the very latest nightly build (dev-1312), you can now do

phenix.refine model.pdb data.mtz place_ions=True elements=Mg,Ca,Cl

the function of which should be fairly obvious.  (You can do this from
the GUI too of course but you'll need to search for those parameters,
they're not displayed by default.)  This will probably work much
better if you use anomalous data, although as Fred notes calcium is a
bit hit-or-miss at this resolution - however I have seen it stand out
clearly in anomalous difference maps of data collected at 1.1Å.
(Also, we're using Phaser and various other tricks, which are far more

Main caveat: bring a book, it is not fast (or run it without anomalous data).

As regards distances, Ed is correct, the nonbonded restraints will
probably dominate, even at 1.6Å.  In this case (from ener_lib.cif in
the CCP4 monomer library), Mg++ has a radius of 0.71, versus 1.14 for


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