Re: [phenixbb] xtriage to double-check symmetry

Hi Frank, There are two types of space group problems: 1. Too much assumed symmetry 2. Not enough assumed symmetry Category 1 is nasty: the structure doesn't refine very well or doesn't solve at all. This is due to the fact that the 'extra' symmetry you have introduced act as constraints on the solution. These symmetry constraints are in fact incorrect, and unless you remove them, things will be not be "im gruenen bereich". Category 2 is a better place to be in. In that case, you can do the RvsR test and inspect the table. If you have an R value for calculated data that is equal to (or very close to) 0, that almost always means that you have missed rotation/screw symmetry somewhere. If on the other hand Robs is near zero, but Rcalc isn't, your data is perfectly twinned. In fact, any significant reduction in Robs with respect to Rcalc, is typically due to twinning. When you miss symmetry, you typically do not notice, unless you look for it. This is due to the fact that the constraints of space group symmetry are turned into something like restraints imposed by inherent symmetry in the data. Turning a constraint in a restraint is typically not very bad, but making a restraint in a constraint, typically makes life difficult. So in short, the only way to find out what's happening, is to remove symmetry operators from your high symmetry solution (i.e. MR in a lower space group), solve and analyze the results. Xtriage can only make specific suggestions which symmetry to add to your model. I do not see how I can make a suggestion which elements to remove without doing the extra refinement steps in lower symmetry space groups. Does this help? Peter 2009/9/17 Frank von Delft :

Then I'm afraid I've totally misunderstood what this does, and I don't see it in the docs either.

It *sounds* like it would take your data and model, and check whether going to higher symmetry would give as good an agreement.

That's obviously not what it does; could you clarify? Thanks! phx

Peter Zwart wrote:

...

Hi Frank,

You can use P65 as well. IN p6522 there are no extra operators (typically),  so not much can be learned (the r value for calculated data will be zero). You do need to have lower symmetry.

HTH

Peter

2009/9/17 Frank von Delft :

...

Hi

We were trying to decide whether a structure is P65 or P6522:  data merges fine in latter, and NCS is perfect, but R/Rfree are significantly worse (32/37-ish vs 23/28 for P65).

So I thought I'd listen to xtriage:  seemed easy since I have both data and model in P6522, and I ran:     phenix.xtriage final.mtz reference.structure.file=final.pdb

I'm not sure it's done anything, though - at least, I can't find the table shown on the 4th-last slide of this presentation:    http://aca.hwi.buffalo.edu/HotNews/twinning/zwart.pdf

Something I said / did not say?  Do I *have* to run it in P1?

Thanks! phx _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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