Creating maps and map coefficients with phenix.maps


phenix.maps is a simple command-line tool for calculating map coefficients from a model and reflections file, with optional FFT to generate an actual map file. The program is largely self-documenting; this section essentially reproduces the command-line output of the program when run without arguments. As of PHENIX version 1.6.4, much of the parameter syntax is identical in phenix.maps and phenix.refine. There is also a GUI for phenix.maps, with separate documentation, but most of the information below applies to both the command-line and graphical versions.

How to run

  • Run phenix.maps without any arguments: just type phenix.maps in the command line and hit Enter. This will creare a parameter file called maps.params, which can be renamed if desired.
  • Edit maps.params file to specify input/output file names, data labesl and the desired maps. It is possible to request as many maps as desired. By default, the file maps.params specifies 5 maps to be created: 2mFo-DFc, 2mFo-DFc with missing Fobs filled with DFcalc, mFo-DFc and anomalous difference maps will be output in MTZ format, and one 2mFo-DFc map will be output in X-plor formatted file.
  • Run this command to compute requested maps: phenix.maps maps.params


  • The scope of parameters 'map_coefficients' defines the map that will be output as Fourier map coefficients. The scope of parameters 'map' defines the map that will be output as X-plor or CCP4 formatted map.
  • To create several maps: duplicate either 'map_coefficients' or 'map' or both scopes of parameters as many times as many maps is desired. Then edit each of them to define the maps.
  • A map is defined by specifying a map type using 'map_type' keyword available within each scope of parameters: 'map_coefficients' or 'map'. The general supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[filled]. For example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, anom. The 'map_type' parser will automatically recognize which map is requested.
  • The program creates an individual map file for each X-plor/CCP4 map defined in the parameters, but it creates only one MTZ formatted file with all Fourier map coefficients in it.
  • The X-plor formatted map can be computed in the entire unit cell or around selected atoms only.
  • Twinning (if detected) will be accounted for automatically. This can be disabled by using "skip_twin_detection=True" keyword.
  • All arrays used in map calculation, for example: Fobs, Fmodel, Fcalc, Fmask, m, D, etc., can be output into a CNS or MTZ formatted reflection file.
  • For those who likes to experiment: bulk solvent correction and anisotropic scaling can be turned off, the data can be filtered by sigma and resolution.

FFT-ing map coefficients

If you already have map coefficients in an MTZ file and just want to run an FFT to produce X-plor or CCP4 map files, use phenix.mtz2map. In most cases this can be run automatically by passing the name of the MTZ file. MTZ files generated by phenix.maps, phenix.refine, SOLVE/RESOLVE, and REFMAC are supported, and additional combinations of map coefficients are possible if defined by the user. By default, output files will take the base name of the MTZ file, with the appropriate map type appended if it can be guessed from the column labels, otherwise a unique integer, followed by the file type extension (.ccp4 or .xplor).

Other map types

The functionality in phenix.maps is intentionally kept simple, but more complex map calculations may be performed in other programs:

  • For isomorphous difference maps (Fobs-Fobs), use phenix.fobs_minus_fobs_map (documentation to be added).
  • For omit maps, including composite omit maps and iterative build omit maps, use the AutoBuild wizard.
  • You can also generate a simple simulated-annealing omit map by deleting the relevant part of the molecule and running phenix.refine with simulated_annealing=True. (This is essentially the same was what is done by AutoBuild, however.)