I am trying to follow the tutorial case Yeast U4/U6.U5 tri-snRNP to learn local refinement. I have two questions regarding the tutorial:
1, when you use the mask to subtract the region you don’t want to refine, do you use the dialated mask to do the subtraction or do you use the original generated in chimera to do the subtraction.
2, about the search range: in the tutorial, it says ‘based on the range of motion seen in the particle from the heterogenous refinement earlier’, I am wondering where in the heterogeneous refinement can I find these parameters.
3, I did the local refinement on the head part, and tried to follow the tutorial, and I got a 4.13Angstrom structure for the head part which is lower than the one the tutorial got. I am not sure what could be the reason or what I can do better.
Thank you and looking forward to your reply.