[buster-discuss] Clarification: Not French Wilson

esserlo at helix.nih.gov esserlo at helix.nih.gov
Tue Nov 25 14:51:13 CET 2014

```Hi,

in my previous e-mail (I don't know what behooved me to do so) but I mixed
up two things that should not be confused as Peter pointed out (see below).

My question simplifies to this:

Based on the observation that Buster refine expects amplitudes and not
intensities (I tried but it complained), I have the option to covert I to F
in the traditional way (here I am using phenix.reflection_file_converter
using defaults) or I can use the option "massage-intensities" which is a
process of altering mostly weak reflections incl. those with negative
intensities using the prior "knowledge" that they all should be positive.
The first time I learned about the formula written down by Peter (|Fnew|) is
when I read it in the book "Data Analysis A Bayesian Tutorial by D.S.
Sivia".

Well, the questions is this: Which option should I use ?

It may matter that I am working with a low resolution data set which likely
has quite a number of weak reflections. If I had a very strong data set, it is
likely that massage-intensities makes no difference whatsoever.

Thanks,

Lothar

Hi Lothar,

Although I do not know the preferences of BUSTER, I thought it would be
good to point out that phenix provides two options.

-1- plain French & Wilson scaling
-2- 'massage intensities'

The first one is an amplitude estimate on the basis of Wilson (a different
Wilson in this case) statistics. This is equivalent to the CCP4 code AFAIK.

The second option is doing something that is obtained when you assume a
flat, improper positive prior on the intensities, resulting in

|Fnew| = sqrt((Io+sqrt(Io**2 +2sigma**2))/2.0).

I derived this myself a while ago and subsequently found that this was (of
course) done by (I think) David, but cannot find the reference at this
point in time.
The beauty of the method 2 is that it is not sensitive to anisotropic
scattering and/or pseudo centering, which can be useful in some cases.

I do not know what buster likes, but it is good to know that there are
several options.

Given that this is a phenix specific email on a Buster mailing list, I have
send this to you and Clemens Vonrhein only to avoid ruffling feathers.

Cheers
Peter Zwart

On 24 November 2014 at 13:11, <esserlo at helix.nih.gov> wrote:

> Hi,
>
>   when I convert my data file from phenix.refine which uses intensities to
> autobuster which requires amplitudes, I have the option to
> "massage-intensities" which is French and Wilson scaling.
> My question is whether French and Wilson scaling should be applied or not.
> Or
> should I always test both ways and pick the one that gives lower R-free
> values?
> This seems like a bit of a trivial question but I could imagine that the
> buster developers have strong opinions about how data should or should not
> be
> treated.
>
> Thanks,
>
>    Lothar
>
> _______________________________________________
> buster-discuss mailing list
> buster-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/buster-discuss
>

--
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P.H. Zwart
Staff Scientist
Berkeley Center for Structural Biology, Science lead
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
SASTBX:  http://sastbx.als.lbl.gov
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
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