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

Nathaniel Echols nechols at lbl.gov
Thu Apr 4 12:18:42 PDT 2013

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,

(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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130404/aefecbd6/attachment.htm>

More information about the phenixbb mailing list