Re: [phenixbb] questions about using experimental phases in phenix.refine

Hi Dave, I’d suggest using the Phenix program phenix.map_to_structure_factors to convert a map to an MTZ file. This will generate HLs with reasonable FOMs. I suspect the problem with what you did before is that the FOMs are all 1, and this isn’t handled well by the MLHL target (this is a guess on my part). We don’t have a vector LS target in phenix.refine - we encourage people to use real space refinement for cryo-EM data. Cheers, Paul

On May 15, 2021, at 10:29 AM, David A Case wrote:

I'm trying to use experimental phases derived from an cryoEM density map do carry out reciprocal space refinement in phenix.refine.

I used phenix.map_box to get the map coefficients, and then the CCP4 program chltofom (with the -colin-phifom flag) to create the HL coefficients from F/PHI computed from the electron density map.

1. If I ask for the mlhl target, I get quite odd target values, e.g. for a 2.9 Å data set:

| normalized target function (mlhl) (work): -5862.311069 | | target function (mlhl) not normalized (work): -6438670043.811632

and attempted refinements more or less destroy my protein and increases both the mlhl target value and the R-factors. Is there an example data set I could access to help me find out what I'm doing wrong? (Using the ml target, as suggested in DeMaio et al, Nature Methods 10:1102, 2013, seems to work well, and has a postive target function, but seems sub-optimal if phase information is available.)

2. Is there a way to do a "simple" least-squares refinement, minimizing sum( w_i * |Fobs_i - Fcalc_i|**2 ) where both Fobs and Fcalc are treated as vectors? Does the ls target perhaps do this if use_experimental_phases=True?

Usual apologies if there is some great tutorial on this that I've not found.

...thanks...dave case

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