[phenixbb] real space refine and nonbonded_weight
pafonine at lbl.gov
Fri Oct 25 11:48:43 PDT 2019
> Dear Developers
> A structure we refined back in 2017, using phenix.real_space_refine on
> a cryoEM map @ 3.7A (version 1.11.1–2575) produces a clashscore of ~8
> but the exact same refinement run with the latest phenix (version
> 1.17.1) generates a clashscore of ~22. Our refinements with the
> latest version on other EM structures tend to generate pretty high
> clashscores too.
> I think i've tracked this down to the nonbonded_weight parameter,
> which defaults to 1000 in the older version, and to 100 in the latest
> At which version did the default change, and is there a reason for
> it? I couldn't find it in the changelog.
yes, we did change nonbonded_weight from 1000 to 100 at some point in
the past. This was based on a quick investigation that I did, details
Hope this answers your question! Get back to us if not.
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