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

Paul Adams pdadams at lbl.gov
Sat May 15 12:35:42 PDT 2021

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.


> On May 15, 2021, at 10:29 AM, David A Case <david.case at rutgers.edu> 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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Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib)
Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov)
Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov)
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