[phenixbb] refinement with anomalous data

Dale Tronrud detBB at daletronrud.com
Fri Feb 6 11:44:02 PST 2015

Hash: SHA1

   What you are confusing is "reflection/parameter ratio" with
"independent observation/parameter ratio".  An independent observation
is one where your couldn't guess the outcome of the measurement before
you made it.  When there is no anomalous scattering you can predict
with great reliability F- once you have measured F+ so you can't count
them both.

   This whole business of counting observations and counting
parameters really doesn't work with nonlinear mathematics so it is
really only a broad rule-of-thumb for us - even when you are careful
in your count.

Dale Tronrud

On 2/6/2015 11:26 AM, Guangyu Zhu wrote:
> What I meant is: I actually don’t have anomalous signal, so when I
> use I+/I-, kind of like I use Imean twice for each reflection. Can
> I do that?  My guess is that the resolution is low, so double 
> reflection/parameter ratio really benefits the refinement,
> although overall the weight for x-ray term is not change, because
> rms bond and angle are similar.
> Newer versions are better for my other refinement with higher 
> resolution, but not this data set.
> Guangyu
> From: Pavel Afonine <pafonine at lbl.gov <mailto:pafonine at lbl.gov>> 
> Date: Friday, February 6, 2015 at 2:12 PM To: Guangyu Zhu
> <gzhu at hwi.buffalo.edu <mailto:gzhu at hwi.buffalo.edu>>, 
> "phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>" 
> <phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>> 
> Subject: Re: [phenixbb] refinement with anomalous data
>> I use same data set for refinement, so Rfree is also marked for
>> same reflection. The only difference is that I chose “Data
>> labels” from Phenix IMEAN or I(+) I(-).
> What I meant is that the IMEAN set is not the same as I(+),I(-) at
> least because the number of reflections in IMEAN is not the same as
> in I(+),I(-).
>> By the way, I use version 1.8.2 for refinement. Newer versions
>> gives higher R/Rfree.
> Should be the other way around...
> Pavel
> _______________________________________________ phenixbb mailing
> list phenixbb at phenix-online.org 
> http://phenix-online.org/mailman/listinfo/phenixbb
Version: GnuPG v2.0.22 (MingW32)


More information about the phenixbb mailing list