A protein is attached to the side chain of microtubule tubeA, but after Helical Refinement it cannot be seen. Besides the possibility that the flexible region is averaged out during helical refinement, are there any other possible reasons? Do you have any good suggestions?
Thank you in advance for your advice.
In addition to flexibility (which you could address with symmetry expansion followed by local refinement), it could also be a matter of lower occupancy (which could be diagnosed with focused 3D classification). Another possibility could be that the additional density manifests at a different helical symmetry than the core of the filament. This could be checked by running helical refinement with progressively lower helical symmetry by e.g. doubling, tripling, etc the rise and twist value that were used.