I now realize that I am confused as to what the mentioned "weight" parameter refers to. The Phenix RSR documentation contains a line that reads "T = Tmap + weight * Trestraints"—if I'm understanding correctly (?), this means a larger "weight" value should yield greater conformity to geometric restraints at the expense of model/map fit. In reality, I observe the opposite trend in my refinements (which is why I assumed it was a "map weight"). Can someone clarify what "weight" (Refinement Settings > "Other Options") refers to?

The reason I am exploring these questions is that Phenix RSR is introducing bond angle outliers into a low-resolution area of a DNA molecule in my model—most of the outliers are not acknowledged as such (by Phenix), and I only become aware of them when the wwPDB validation tells me they are there. I assumed this was the result of overfitting to the map because setting "weight" to 0.0 prevented these outliers from appearing, but at the expense of map-model fit in the remainder of the structure (which is why I wanted to apply different weights to different segments of the model).

Thanks,

Josh

On Sun, Sep 12, 2021 at 12:21 PM Josh Cofsky <josh.cofsky@gmail.com> wrote:

Hi all,

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!
-Josh

(also, apologies if this is a duplicate message...still trying to figure out the phenixbb listserv)