[phenixbb] WAS: changing TLS groups mid refinement

Peter Zwart PHZwart at lbl.gov
Mon May 17 16:20:53 PDT 2010

> Now from what you are saying I understand that there is some possibility
> to get into using non-truncated data with phenix?  And not only that, it
> seems to be the default?

You make it sound like it is a bad thing. The effect of restraint
weights (ADP, geometry) has most likely a much bigger impact on the
final structure then a small fraction of smallish intensities (*)

The French and Wilson procedure does circumvent issues with negative
intensities, but depends on some prior knowledge of the intensity
distribution and uses this to estimate the 'error free amplitude'. It
all sounds nice, but it is not without trouble. If one has pseudo
translational symmetry for instance, the basic wilson prior isn't
valid. I agree at that smallish intensities are useful (if not
essential in that case, depending on the degree of the PTS), but a
bayesian update with an incorrect prior might even be worse. Also, why
limit oneself to updating negative intensities? This is a fairly
arbitrary decision rule. Also, how does one update? Do we update to
the most likely posterior intensity or to the most likely posterior
amplitude? These need not be the same.

I fully agree with Pavel that a solution should be pursued and I also
agree that the effort/payoff ratio should be used for ranking
purposes. There is a intensity massaging option available in phenix,
it is not default, well hidden and not for the faint of heart for
reason stated above.



(*):  when the fraction is not small, but fairly sizeable due to
pseudo translational symmetry, I definitely wouldn't want to have a
French and Wilson procedure let loose on my intensities, but an ML
intensity target that can deal with this kind of data is the only

> I suspect that French&Wilson statistics is actually applied by phenix
> internally if the supplied mtz-file only has intensities.  If that is
> not the case, the problem is more serious than I thought.  Otherwise it
> would take deliberate user effort to get into trouble, since
> TRUNCATE=YES is the default of the corresponding CCP4 program.
> Ed.
> --
> "I'd jump in myself, if I weren't so good at whistling."
>                               Julian, King of Lemurs
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:     http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net

More information about the phenixbb mailing list