[phenixbb] table 1 no CC values, selenomethionine occupancy refinement

[Nathaniel Echols]

On Thu, Apr 4, 2013 at 12:10 PM, Francis E Reyes <Francis.Reyes at colorado.edu
> wrote:

> Does phenix.refine substitute the wavelength dependent f'/f'' when
> computing f for atoms in refinement?


No - I added a wavelength parameter a couple of months ago, but that is
used for ion picking, it doesn't change the input model.  (Although some of
us think that might be a good idea.)  phenix.maps and
phenix.find_peaks_holes *do* use the wavelength parameter in this way,
however.

(maybe it was read from a properly formatted mtz)


MTZ files always contain a wavelength - the problem is that we can't be
sure whether this was set correctly or not.  I suspect that MTZ files
produced by CCP4 processing tools will have the correct wavelength, but the
downstream programs may choose to ignore this.  (Most of our tools default
to writing a wavelength of 1.0; I've started to fix this but it's going to
take a while.)


> Or does it assume CuKa scattering factors?
>

No, in phenix.refine atoms never become anomalous unless you specify the
anomalous groups.

-Nat
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