I'm using phenix.real_space_refine to refine a model into a cryo-EM map. My local map resolution is highly variable across the molecule, and using a single map weight (the parameter shown in the Refinement Settings > "Other Options" in the GUI) on the whole model leads to poor map-to-model fit in some locations and overfitting in others. Potential solutions could be to:

1. assign different map weights to different segments of the model (based on a user-specified atom selection)

OR

2. perform iterative refinements with different weight settings, holding different (user-specified) segments of the model fixed during each iteration (I suspect this isn't possible based on Pavel's message here: http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html)

Is either of these approaches (or another one that accomplishes the same goal) possible? I am using the Phenix GUI, but if this is only possible in command line, and you're willing to share an example command that accomplishes either of these tasks, please let me know.

Thanks!