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tjlane / thor

support code for x-ray scattering experiments
GNU General Public License v2.0
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solvent inclusion in scattering simulation #16

Closed dermen closed 10 years ago

dermen commented 10 years ago

After attending this IUCr conference, receiving feedback from the community, and also just thinking about the future and moving towards biomolecules, I think it will quickly become critical to include solvent in the scattering simulations. How close are we to being able to do this ?

I am sure there are several techniques for doing this, and how to be most efficient about it is still unknown to me. We could start by creating a somewhat small layer of water (or whatever solvent) surrounding the particle and equilibrating, and then using that in the simulation. I say small shell because long range correlations between the particle and the solvent are less likely to exist and corrupt the signal.

Anyway, I guess this could be done separately from thor

tjlane commented 10 years ago

I strongly suspect you're right -- esp since this makes a huge difference in SAXS/WAXS. It should make a difference as well in CXS.

Check out this cool new paper Fred linked me a month or so ago about WAXS: http://www.cell.com/biophysj/abstract/S0006-3495%2814%2900610-9

That's definitely a gold-standard approach, but would be fairly easy to implement. Maybe we should give it a shot for e.g. Lysozyme?

We may have a need to do this in the near future to predict SAXS for a project in the pande lab -- maybe we can combine forces? @dermen is this an immediate need or more of a long term thing to think about?

dermen commented 10 years ago

I would say I can start working on this in a month or so, and I would like to have some results within maybe 2 months, seem reasonable ? Not an immediate need, but certainly something I have noticed is going to be critical for e.g. grant proposals , not to mention beamtime proposals

tjlane commented 10 years ago

I'm going to close this b/c I don't think it belongs as part of thor, but we should continue the conversation elsewhere.