[phenixbb] convergence in Phenix real space refinement
Robert Oeffner
robert at oeffner.net
Fri Oct 20 00:29:24 PDT 2023
Thanks Pavel, In one test example I noted that "moved from start" didn't
change much after about 12 macro cycles. This would then be a necessary
but not sufficient condition for convergence If I understand you
correctly. Would there be any other statistics indicating convergence?
In my test example CCmask hardly changed at all.
Rob
On 20/10/2023 04:03, Pavel Afonine wrote:
> Hi Rob,
>
>> I'm curious to know when convergence has been obtained in
>> phenix_real_space_refine. I see the number "moved from start" in the
>> log file and assume that once it doesn't change much after several
>> macro cycles then convergence has been obtained when refining a
>> structure. True? What is that value based on, the RMSD between the
>> initial structure and the final structure? I didn't find this
>> documented in the 2018 publication of the program.
>
> phenix.real_space_refine runs a set number of cycles that you can
> adjust. In the log file it reports the rmsd between the initial and
> current model. While this number can give you some idea about the
> amount of model movement between cycles, it also may hide some useful
> information: for example, if you refine a large structure and only a
> few residues flipped their side chain conformations during refinement,
> then this overall number probably won't tell you this.
>
> Pavel
>
>
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