Ticket #260 (closed feature: shelved)

Opened 5 years ago

Last modified 21 months ago

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:1 Changed 5 years ago by ajj

  • Milestone changed from Analysis Wish List to Wish List

comment:2 Changed 4 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.

comment:3 Changed 21 months ago by srkline

  • Status changed from new to closed
  • Resolution set to shelved

Analysis items shelved

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