These are in hydrophobic pockets., it seems. Maybe you have put bulk solvent in there, but the spaces are really empty? Some folks add very low occupancy waters in there to stop bulk solvetn additions as a work around.

On Mar 13, 2024, at 11:51 PM, Andrea Smith <andrea.smith@uochb.cas.cz> wrote:

Hi,

i am working on a structure where I have a few relatively big red blobs (please see attached print screens with maps at 1.2 and 3.5 rmsd). The data were processed at BESSY, mtz was used in Phaser and refined in phenix.refine.
Can someone explain why this happens (and whether it is an issue)?

Thank you,
Andrea <red_blob.png><red_blobs.png>_______________________________________________
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