phenix.development.fem: compute Feature Enhanced Map (FEM)

Description

This is a developmental version and it will be such until official publication in peer reviewed journal. The program reads PDB model, reflection data (Fobs or Iobs) and R-free flags, if available. Then it computes {2mFobs-DFmodel, Phase_model} map, which is subject to FEM procedure.

Output is MTZ file with four sets of Fourier map coefficients:

• 2mFoDFc,PHI2mFoDFc: usual {2mFobs-DFmodel, Phase_model} sigma-a weighted synthesis. No anisotropy correction or filling missing data.
• 2mFoDFc_FilSharp,PHI2mFoDFc_FilSharp: same as above but B-factor sharpened, anisotropy corrected and missing Fobs are modeled.
• KICK,PHIKICK: "kick" map
• FEM,PHIFEM: Feature Enhanced Map

Of real interest are only 2mFoDFc,PHI2mFoDFc (which is output to compare with FEM map) and FEM,PHIFEM - the main result of running this tool. The other map coefficients are present for information or debugging.

Important:

FEM map is not expected to contain any more signal than the original starting map. The new map is expected to contain less noise and all the available signal equalized in strength, so both strong and very weak signal are available for interpretation at the same threshold contouring level.

% phenix.fem model.pdb data.mtz
% phenix.fem data.mtz model.pdb label=Fobs
% phenix.fem model.pdb data.mtz scattering_label=neutron

Graphical user interface is available

Currently only {2mFobs-DFmodel, Phase_model} map can be used in FEM protocol and it has to be computed internally by the program (that is no user-specified map coefficients can be used).

Latest presentation of FEM methodology:

http://www.phenix-online.org/presentations/fem.pdf

Publication in Computational Crystallography Newsletter (front page):

http://www.phenix-online.org/newsletter/CCN_2013_07.pdf