Re: [phenixbb] zero B-factors

Hi Morten, POLYGON is the tool for this. Definition "too low/high" is relative and depends on resolution. Pavel On 11/25/13 4:29 AM, Morten Grøftehauge wrote:

It would be nice if the validation procedures looked for B-factor outliers that were too low as well as too high. A very low B-factor can be indicative of the wrong atom, e.g. a water molecule that is actually an ion.

Morten

On 18 November 2013 21:38, Pavel Afonine mailto:[email protected]> wrote:

If you see this problem using the latest Phenix version then please send me files (off-list) necessary to reproduce it and I will investigate.

If interested what was the "problem" causing zero B-factors please see below.

Thanks, Pavel

In a nutshell the problem is this. Assuming total model structure factor is (for simplicity):

F ~ exp(-Boverall_scale * s**2) * exp(-Batoms * s**2)

it's clear that any combination of Boverall_scale and Batoms that maintains Boverall_scale+Batoms=const will not change total model structure factors (and therefore R-factors, maps, etc).

The new bulk-solvent and overall scaling algorithm that we implemented sometime in April 2012 and that went into 1.8_1069 originally did not care about returning isotropic component of Boverall_scale back to atoms (Batoms):

http://journals.iucr.org/d/__issues/2013/04/00/dz5273/__dz5273.pdf http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf

In fact, it assumed that overall contribution (overall B that is equal for all atoms) should stay in Boverall_scale (indeed, why keep common B in all individual atomic B-factors!?), and the rest goes into Batoms. This behavior typically generates user concerns about "too small" B-factors.

An alternative agreement is to postulate that the matrix Boverall_scale is traceless meaning that overall B-factor goes into individual atomic B-factors. This behavior occasionally generates user concerns about "too large" B-factors.

A few months later (sometime in end summer/fall 2012) we changed scaling behavior such that overall B-factor stays in individual atomic B-factors.

All in all, either way is correct and a matter of agreement and preferences, but definitely not a bug.

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-- Morten K Grøftehauge, PhD Pohl Group Durham University

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