[phenixbb] Fwd: Re: anisotropic induced noise amplification

[Pavel Afonine]

Hi,

I realized Randy's reply did not go to the mailing list, so I'm 
forwarding it now.

Pavel


-------- Original Message --------
Subject: 	Re: [phenixbb] anisotropic induced noise amplification
Date: 	Mon, 7 May 2012 09:49:57 +0100
From: 	Randy Read <rjr27 at cam.ac.uk>
To: 	Pavel Afonine <pafonine at lbl.gov>
CC: 	developers at phenix-online.org <developers at phenix-online.org>, Peter 
Zwart <PHZwart at lbl.gov>



In the absence of an answer from Peter (who implemented this and 
therefore ought to know best), I'm pretty sure that the idea is to 
measure how much difference there is in the amount of signal in the data 
that have received the biggest anisotropy corrections, compared to the 
ones that have received the smallest anisotropy corrections.  If there's 
very little signal in the data that have been scaled up the most, then 
the noise is being amplified (nearly-random amplitudes have gone from 
being relatively small to the same size on average as the well-measured 
amplitudes).

But  what the Z-scores mean is not at all clear from that output, and 
I'm not aware that Peter has written anything describing this.

This amplified noise is what I suspect is creating problems in 
phenix.refine refinement with highly anisotropic data, because if the 
experimental sigmas are ignored then the program doesn't know (after 
anisotropic scaling) which amplitudes of a comparable size contain 
signal and which are essentially noise.  Anisotropic truncation gets rid 
of it, which would explain why refinement works better with 
anisotropically-truncated data.

Randy

On 6 May 2012, at 20:21, Pavel Afonine wrote:

> Hi,
>
> did anyone address this post? I'm interested to know the answer 
> myself: I have absolutely no idea what is this.
>
> Pavel
>
> -------- Original Message --------
> Subject: 	[phenixbb] anisotropic induced noise amplification
> Date: 	Wed, 2 May 2012 16:06:55 -0500
> From: 	James Thompson <Thompson.James at mayo.edu>
> Reply-To: 	PHENIX user mailing list <phenixbb at phenix-online.org>
> To: 	phenixbb at phenix-online.org
>
>
>
> Anyone willing to summarize Xtriage's algorithm that determines 
> whether "/anisotropic induced noise amplification/" is present in 
> diffraction data?  What is this noise amplification?  Is it 
> anisotropic correction factors that over-fit the data thereby inducing 
> noise?
>
> Many thanks,
> Jim T
>
> ----------------    Anisotropy analyses     ----------------
>
> Anisotropy    ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) :  3.596e-01
>                           Anisotropic ratio p-value :  0.000e+00
>
>      The p-value is a measure of the severity of anisotropy as 
> observed in the PDB.
>      The p-value of 0.000e+00 indicates that roughly 100.0 % of 
> datasets available in the PDB have
>      an anisotropy equal to or worse than this dataset.
>
>
> For the resolution shell spanning between 2.36 - 2.20 Angstrom,
> the mean I/sigI is equal to  3.37. 42.2 % of these intensities have
> an I/sigI > 3. When sorting these intensities by their anisotropic
> correction factor and analysing the I/sigI behavior for this ordered
> list, we can gauge the presence of 'anisotropy induced noise 
> amplification'
> in reciprocal space.
>
>   The quarter of Intensities *least* affected by the anisotropy 
> correction show
> <I/sigI>                 :   3.82e+00
>     Fraction of I/sigI > 3   :   5.01e-01     ( Z =     3.59 )
>
>   The quarter of Intensities *most* affected by the anisotropy 
> correction show
> <I/sigI>                 :   2.02e+00
>     Fraction of I/sigI > 3   :   1.84e-01     ( Z =    10.78 )
>
> *The combined Z-score of    11.36 indicates that there probably is 
> significant*
> *systematic noise amplification that could possibly lead to artefacts 
> in the*
> *maps or difficulties in refinement*
>
> <Attached Message Part.txt>

------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: rjr27 at cam.ac.uk 
<mailto:rjr27 at cam.ac.uk>
Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk

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