Hi Dave, could you please send me the data and model files (off-list, directly to my email), and tell residue numbers that are close to the residual density in question? I will investigate once I have the files. Most likely it's a footprint of bulk-solvent mask set in regions where there is actually no any solvent. Thanks, Pavel On 6/27/12 1:29 AM, David Briggs wrote:
Hi all,
I'm refining a couple of structures of the same protein (well, point mutants) and I am consistently seeing large (6sig) negative difference map peaks within some cavities within my protein, present in both the datasets. As far as I understand, this is because the bulk solvent scaling parameters are either incorrect, or being incorrectly applied. I have tried a few things like applying the "Refine solvent mask (slow)" options, all to no avail.
Resolution is 2.2Å and 2.5Å. Experimental phasing, Xtriage reports no abnormalities in the data.
Is there anything that I am missing? Do I need to worry about this?
Regards,
Dave