Dear all,
we are working on a dataset from a homo-trimeric protein. Until now we have very successfully refined the structure to good resolution applying C3 symmetry in RELION.
However, we also have a sample from this protein that contains a low affinity binding substrate and we would like to do a classification to see if there are some subunits showing the expected conformational change due to substrate binding. The point is, that we do not expect the ligand to bind to all three monomers of one particle but that the conformational change might only happen in one of the monomers of a particle. Therefore, normal 3D-classification seems unrewarding and a masked classification would suffer from the aspect, that we always only look on one of the monomers ignoring two-thirds of the data.
We were thinking that it might be helpful if we somehow triplicate the particles, each rotated by 120° to get all of the three monomers from one particle inside the mask. Is there any clever way to do this in RELION or does anybody else has a good idea how we could proceed?
Best,
Julian
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