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

Nathaniel Echols nechols at lbl.gov
Thu Apr 4 11:39:43 PDT 2013

On Thu, Apr 4, 2013 at 11:22 AM, Georg Mlynek <georg.mlynek at univie.ac.at>wrote:

> 1a. Providing the XDS_ASCII.HKL to phenix tableI works perfect, however
> there are no values written for CC1/2. The same file in
> phenix.merging_statistics I get the CC1/2. Am I missing something?

No, I am.  Sorry, will fix this ASAP.

1b. The only value phenix tablel one takes from INTEGRATE.LP (i guess
>  CORRECT.LP will work too) is the wavelength - true?

I'm not sure which specific files from XDS will actually work, but in
general, yes, the wavelength is the only thing I extract from the
integration log file.  (Unfortunately this is the one parameter on which we
really depend on logfiles, since the wavelength is - inexplicably - not
reliably propagated in reflection files.)

2. I see some negative density around the seleniums in my selenomethionine
> labeled protein. I guess this is due to radiation damage. Is the accepted
> standard to do occupancy refinement for just the sidechain, or just parts
> of the sidechain, the whole residue  or just leave it like it is.

This seems like a matter of personal preference, but I would definitely
*not* refine the occupancy of the entire sidechain unless I was modeling it
as a mix of MET and MSE to reflect partial incorporation.  So there are
several options:

1) refine the occupancies for SE atoms alone
2) leave them alone
3) refine alternate conformations

I prefer (1), but it's difficult to know exactly what the difference map
holes mean; they could simply be Fourier artifacts.

A less conventional option is to refine f' and f'' for the SE atoms, but
leave the occupancies at 1.  I'm still a little confused about how f' and
occupancy are correlated*, but in my experience the anomalous refinement
soaks up most if not all of the difference in occupancy.  The problem right
now is that you can't deposit these parameters in the PDB, but hopefully
that will change soon.


(* A follow-up question for more knowledgable folks: could the large
dispersive difference at the K edge be reflected as apparent partial
occupancy, or am I misunderstanding the effect on scattering?)
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