[phenixbb] Restricting real-space refinement and weights to specific atom selections

Josh Cofsky josh.cofsky at gmail.com
Sun Sep 12 18:42:25 PDT 2021

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).


On Sun, Sep 12, 2021 at 12:21 PM Josh Cofsky <josh.cofsky at 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)
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