[phenixbb] phenix.maps: a command line tool to compute various maps

Pavel Afonine PAfonine at lbl.gov
Thu Feb 4 21:21:55 PST 2010

Starting PHENIX nightly build version 1.6-295 (or whatever next 
version), the new command line tool


is available. As the name suggests, this is the tool for map 
calculation: regular (p*Fobs-q*Fcalc) or maximum-likelihood 
(p*mFobs-q*DFcalc), with any user-defined coefficients p and q, as many 
as requested.

For example, 2mFo-DFc, 3Fo-2Fc, mFo-DFc, Fc, Fo, Anomalous difference 
maps can be all computed at once. Also, a user has a full control over 
various map calculation parameters, such as filling missing Fobs with 
DFc, computing kick maps, etc. Maps can be output in X-plor formatted 
files or as Fourier map coefficients in MTZ formatted file. X-plor 
formatted maps can be computed for the whole molecule/unit cell or any 
selected part of the structure.

This new tool is meant to be a replacement for current practice of 
computing the maps using phenix.refine (although, phenix.refine still 
output maps as before).

For more information and usage examples simply run phenix.maps .

This is available from PHENIX GUI too (thanks Nathaniel Echols).

For usage instructions and quick manual type phenix.maps and hit Enter.

Please let me know should any questions or problems related to using 
this tool arise.


P.S. Below is the result of running phenix.maps:

phenix.maps: a command line tool to compute various maps.

How to run:

  1. Run phenix.maps without any arguments: just type phenix.maps in the 
     line and hit Enter. This will create a parameter file called 
     which can be renamed if desired.

  2. Edit maps.params file to specify input/output files and the desired 
     It is possible to request as many maps as desired.

  3. 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' 
    the map that will be output as X-plor 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 
    within each scope of parameters: 'map_coefficients' or 'map'. The 
    supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[kick][filled]. For
    example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, 
    The 'map_type' parser will automatically recognize which map is 

  - The program creates as many files with X-plor formatted maps as many 
    formatted maps is requested, and 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 
    selected atoms only.

  - Kick maps and missing Fobs filling is done (if requested) as 
described in
    Adams et al. (2010). Acta Cryst. D66, 213-221.

  - Twinning (if detected) will be accounted for automatically.

  - 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.

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