Opened 6 years ago
Closed 3 years ago
#260 closed feature (shelved)
Simple simulator for proteins
| Reported by: | srkline | Owned by: | srkline |
|---|---|---|---|
| Priority: | major | Milestone: | Wish List |
| Component: | Analysis | Keywords: | |
| Cc: | Blocking: | ||
| Task: |
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 (3)
comment:1 Changed 6 years ago by ajj
- Milestone changed from Analysis Wish List to Wish List
comment:2 Changed 6 years ago by srkline
comment:3 Changed 3 years ago by srkline
- Resolution set to shelved
- Status changed from new to closed
Analysis items shelved
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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.