Ticket #260 (closed feature: shelved)
Simple simulator for proteins
| Reported by: | srkline | Owned by: | srkline |
|---|---|---|---|
| Priority: | major | Milestone: | Wish List |
| Component: | Analysis | Keywords: | |
| Cc: | Task: | ||
| Blocking: |
Description
For proteins, they are not necessarily a "sphere", but the user may know a reasonable Rg value to expect. So can we make a simulator (or a function) that will allow inputs of: concentration (mg/ml), Rg (or MW in kDa) and a solvent composition. We might be able to assume a "typical" SLD of the protein, and then a background based on the solvent composition. Then there should be enough to do a simulation of the scattering (how do I simulate the solvent scattering??) and get a realistic idea of how many counts you get above background -- and what the subtraction would look like for a given counting time.
Change History
comment:2 Changed 3 years ago by srkline
I think I've got the pieces for this - to be able to estimate Rg as a function of number of AA in the protein (and estimate number of AA from the MW in kDa). Also have empirical relations of the SLD of proteins and DNA/RNA as a function of H2O/D2O in solvent, including exchangeable hydrogen.
