Hi Sjors,
I'm working with a membrane protein and the structure shows
better-resolved features in the extracellular portion, compared to the
transmembrane portion. I believe that the resolution of the
transmembrane region is compromised because of a combination of two
factors. First, most of the protein mass is extracellular and that
region thereby dominates the alignment. Second, there might be some
degree of flexibility where the extracellular portion of the protein
meets the transmembrane portion.
Can you suggest a strategy to improve the resolution in the
transmembrane region? Perhaps using a soft-spherical mask around this
region during 3D refinement? It's important to note that the protein
essentially looks like a rod protruding from the membrane, and I have
good angular coverage of the side views.
Thanks,
Joel
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