[phenixbb] Global real-space refinement

Pavel Afonine pafonine at lbl.gov
Mon Apr 27 16:56:11 PDT 2015

Hi Oleg,

> I have a question. What does trigger Global real-space refinement ?
> I never seen it before except one structure I am currently working on.
> Also I do not see any options that switch on/off "Global real-space refinement "
> Please advise

it is a bit in flux at the minute as I keep changing underlying code and 
decision making strategies; the snapshots of these changes get into 
nightly builds and so one may observe some incoherent behavior from 
version to version. As you observe it is enabled by default but it does 
not always run. It runs if certain conditions on current model and data 
quality are met; also, if a run deemed unsuccessful phenix.refine will 
revert the result. At present these conditions are hard-wired in the 
code and you cannot alter them. This is going to change in next days 
(realistically weeks).

If you want to refine against the map you can use 
phenix.real_space_refine that offers a broad array of options that are 
specific to map-model fitting, as documented here:



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