Hi Joel,
We have had good results doing exactly what you suggest: make a soft mask
around the region that you want to improve (it may be any shape, but
values should be in [0,1], 1 being what you want to keep, 0 being what you
want to mask away). You can provide this 3D mask on the auto-refine (or
Class3D) GUI.
If the masked out region is small compared to the entire molecule then it
may be better to perform only local angular searches around angles
assigned without any mask.
HTH, S
> 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
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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