On Thu, May 30, 2013 at 7:09 AM, Heather Condurso
I have a similar issue. My data is nearly perfectly twinned so Xtriage usually fails to find any twin law. However when I solve the structure in the lower symmetry space group with twinning my maps look beautiful. In the higher symmetry space group, only 3 of the 6 monomers fit into nice looking density. I simply use generate table 1 and uncheck the box so it won't regenerate R factors. The discrepancy between the R-factors is however much more significant than 2%. From refine I get 18/22 and from table1 28/31.
That's actually a little surprising that Xtriage wouldn't work - would you be willing to send us the data? Keep in mind that if you have perfect twinning and refine with the twin law, I think the maps will look beautiful pretty much by definition, because of the model bias. (Which doesn't mean that you did it wrong - the R-factors sound realistic - you just need to be very careful and make lots of omit maps.) It helps to have actual examples when warning against the dangers of twin refinement and model bias in general, so here's one (attached). This map isn't beautiful, but it matches the model very closely, including the complete lack of sidechains. Another Phenix user got this result by accident with a mostly-if-not-entirely incorrect MR solution - fortunately the combination of missing sidechain density and relatively high R-free (~40%) prompted him to email us. I suspect that if we searched the PDB we'd find an actual published example (especially considering how many spurious ligands have been found there). (Sorry to sound like a broken record here, but this keeps coming up in emails and workshops - perhaps we need better validation tools.) -Nat
