[phenixbb] Fwd: Re: anisotropic induced noise amplification

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 To: Pavel Afonine CC: [email protected] , Peter Zwart 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 Reply-To: PHENIX user mailing list To: [email protected]

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 : 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 : 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*

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------ 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: [email protected] mailto:[email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk