Hi Vincent, - I would add that ion and refine its occupancy and anisotropic ADPs... Oh, I see, the resolution is 3.4A, well, then I would try first isotropic ones. - if the data set you are using contains Fobs(+) and Fobs(-), (and not merged Fobs_merged = 0.5*(Fobs(+) + Fobs(-))), I would refine f' and f'' of the anomalous scatterer. After having done this, check if the residual density is clear, and keep in mind that unbalanced syntheses may have Fourier truncation ripples around heavy atom, see relevant discussion here: http://www.mail-archive.com/[email protected]/msg14835.html and some pictures here: http://www.phenix-online.org/presentations/latest/pavel_maps.pdf In general, getting rid of an unmodeled density is good in a sense that it has a potential to improve the density everywhere else and you may better model other some other parts of your structure, so you get a better model overall. Let me know if you need any help with trying the above suggestions. Good luck! Pavel. On 8/11/10 5:56 PM, vincent Chaptal wrote:
Hi,
the refinement of my structure brings me to a new point where I would appreciate any input. - I solved the structure by molecular replacement. - The refinement looked good, I was almost ready to deposit but there always was a fairly big blob of density that i couldn't explain, loosely coordinated to the protein and far from the active site.
To try to identify what it could be, i calculated an anomalous difference map (data collected at 1A) and I see a peak right in the middle of this density. I have BaCl2 in my crystallization solution so it is the likely guilty ion! (and with further look, it looks like a loose metal site)
So now, I want to refine with Barium in the density and I was wondering what was the best way to do it, and since there is anomalous signal, why not use it? * I updated to the new version of phenix and it reads I+ and I- (while the previous version didn't) but under the refinement settings, the target function ML-SAD is still for developers only. Is it a good idea to use the anomalous Is for refinement, or: * should I re-run Phaser-EP to have phases to use in phenix.refine, or: * should I not bother, the signal is weak anyway (1 barium/ ~400 residues) and continue with my non-anomalous scaled dataset and use the anomalous signal only for a figure to explain why I put the metal here.
(resolution of 3.4A, quite anisotropic)
I can also try everything but I'd like to understand what would be best. Thanks very much for your help vincent