Hi Oli,
Thanks for the quick reply. I have not tried Relion. We suspect occupancy could be an issue. I’ll give Relion a try. Local refinement results are below. It’s much “better” in terms of more visible density at a low threshold but if I want to remove more noise (assuming this is the micelle belt) around the outer membrane protein by increasing the threshold then the density of the flexible protein disappears. The overall resolution of the outer membrane protein also takes a hit. The parameters I used for local refinement were defaulted, with the exception of the mask parameter. I set this to static. I supplied a mask around the complex to try to get rid of the micelles. The mask also had default parameters with the exception of the soft padding I set to 19.
