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NMRLipids / MATCH

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Update calc_FORM_FACTOR.sh #55

Closed hsantila closed 5 years ago

hsantila commented 5 years ago

The bulk density is needs to be calculated over the entire profile. Otherwise the system can end up with a "net charge" and the form factor will deviate from zero at small q.

ohsOllila commented 5 years ago

I do not fully understand this.

In my understanding, the bulk density in the form factor equation is the scattering length density in bulk water, not the average density of water, see e.g. https://doi.org/10.1007/s00232-010-9254-5. X-ray experiment is measuring the contrast of the electron density with respect to the electron density in bulk water. The total electron density in the lipid region does not have to be the same as in bulk water, therefore the form factor does not have to be zero at zero q.

In conclusion, I think that the bulk density should be the density in bulk water, which was taken as the last point in the density profile in the code as bulkDENS=$(tail -n 1 electronDENSITY.xvg | awk '{print $2}').

ohsOllila commented 5 years ago

I have moved the discussion to issue, which I did not notice before: https://github.com/NMRLipids/MATCH/issues/56