Question about hydration layer and normalization for BIFT in RAW

[Feng Yu]

Hi Jesse,

I am generating SAXS data use existing PDB files with FOXS and do not consider the hydration layer. Will the RAW API consider the hydration layer when generate the P(r) curves? In addition, the gi_ift.p in API is not normalized, even if divided by the sum of the curve. Could you tell me which attribute stores the normalized P(r) curve?

Thank you.

Best

Feng Yu

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Feng Yu Ph.D

Postdoctoral Fellow

Lawrence Berkeley National Laboratory

[Richard Gillilan]

Hi Feng Yu,

FoXS does account for the hydration layer. You can find a description of how they do it in

Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A (2013) Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments. Biophysical Journal 105:962–974.

P(r) is simply the Fourier transform of q^2*I(q). It includes the hydration layer.

It is not usually normalized and is equal to the 4pi r^2 weighted probability of finding electrons a distance r apart. It is also a histogram of the number of all possible electron pairs. 

The integral of P(r) is I(0). So that should be the normalization you seek. It is reported in the GUI when you compute a P(r) function. 

The best description I have found of P(r) can be found in this reference:

Glatter, O. The Inverse Scattering Problem in Small-Angle Scattering. in Neutrons, X-Rays, and Light: Scattring Methodds Applied to Soft Condensed Matter (2002).

Hope this helps.

Richard

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[Jesse Hopkins]

Hi Feng Yu,

I’ll add to what Richard said. The P(r) function will include the hydration layer if your scattering profile includes the hydration layer. So if, for example, you were to use an in-vacuum calculation of the scattering profile of a macromolecule (which CRYSOL can provide, as can FoXS run via the command line I believe) then the P(r) function generated from that wouldn’t include hydration. If, on the other hand, the scattering profile includes the hydration layer then that will be included in the P(r) function.

On the question about normalization. The normalized P(r) function is not saved. However, as Richard says the standard normalization factor for the P(r) function is the I(0) calculated from the P(r) function, so you can easily recreate it by calculating P(r)/I(0). You can access the P(r) I(0) value from the api in the same way you’d get other metadata, described here:

https://bioxtas-raw.readthedocs.io/en/latest/api/getting_started.html#accessing-ift-metadata

All the best.

- Jesse

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Jesse Hopkins, PhD

Deputy Director

BioCAT, Sector 18

Advanced Photon Source

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