[phenixbb] FEM map calculation without model?

Pavel Afonine pafonine at lbl.gov
Tue Apr 28 13:53:15 PDT 2015

Hi Oliver,

> Is there any way to apply the local map sharpening and histogram equalization procedures described as part of the FEM map generation procedure (described in “FEM: feature-enhanced map”, Afonine et al,mActa D71 2015) to an MTZ containing amplitudes and phases only, without a model (e.g. as generated by phenix.map_to_structure_factors)?

individual relevant tools (that are described in FEM paper) are 
available in cctbx can and be put together to do this; this requires 
knowing cctbx and some programming. There is no end-user tool to do this 

This page


has all the scripts etc that we used to prepare all illustrations for 
FEM paper. Essentially you can find an example for using all individual 
components described in FEM paper (such as HE, sharpening, etc).

> I would like to see if these different approaches to map modification are useful for improving maps derived from cryoEM. I guess there is no way to do the random map perturbation part of the FEM procedure without a model, but the sharpening and histogram equalization seem like they might be applicable?

We are working on this but when the ready-to-use tool will be available 
that I don't know.


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