On Tue, Oct 25, 2011 at 3:20 PM, Pete Meyer <pame...@mcw.edu> wrote: > This is probably an idea that has already been tried (or discarded as > unsuitable for reasons that don't occur to me at the moment) - but why not > start with good crystals (such as lysozyme) and deliberately make them > worse? Exactly how would depend on what kind of methods you were trying to > develop - but I'd imaging "titrating in" organic solvents/detergents would > be able to turn a well-diffracting crystal into a poor one (with a known, or > at least knowable, answer). Deliberately causing radiation damage, or using > known poor cryo-conditions would also work - probably the type of "badness" > in the data would be different. > > I don't think you'd be able to tune solvent content or number of anomalous > scatterers by damaging good crystals. This would also require a decent > number of crystals (but lysozyme is reasonably inexpensive). But making good > crystals from bad ones is difficult - making bad ones from good ones > shouldn't be. > > Any ideas why this wouldn't work (or citations where it did)?
It probably depends on what kind of methods you are trying to develop, but there are any number of reasons why it wouldn't be a complete substitute for bad data found in the wild (you've already listed a couple), all of them essentially coming down to the same problem: you're limiting what kind of imperfections and pathologies you'll see. How do you get a crystal that is just slightly split, for instance? Or one that diffracts to high resolution but has a mosaicity of 2.5 degrees? I can think of plenty of other special cases, and the data processing people probably have dozens of ideas. We could spend a month abusing lysozyme crystals and still not come up with anywhere near the diversity that the community can generate with their membrane proteins, glycoproteins, RNA, etc. This is true for everything from data processing to refinement. (Fortunately, for refinement we already have most of what we need in the PDB.) That doesn't mean it's not a good idea anyway; I've considered doing something similar to generate pairs of realistic high-resolution and low-resolution data. (Probably not using lysozyme - it's much too small to be representative of the average 4A structure.) It's a good summer project for a capable undergraduate student, if you have synchrotron time to burn. -Nat
