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

Josh Cofsky josh.cofsky at gmail.com
Sun Sep 12 12:21:21 PDT 2021

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)
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:

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.


(also, apologies if this is a duplicate message...still trying to figure
out the phenixbb listserv)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20210912/6510801f/attachment.htm>

More information about the phenixbb mailing list