FFT-ing map coefficients

Other map types

List of all mtz2map keywords

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

• 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.)

List of all mtz2map keywords

------------------------------------------------------------------------------- 
Legend: black bold - scope names
        black - parameter names
        red - parameter values
        blue - parameter help
        blue bold - scope help
        Parameter values:
          * means selected parameter (where multiple choices are available)
          False is No
          True is Yes
          None means not provided, not predefined, or left up to the program
          "%3d" is a Python style formatting descriptor
------------------------------------------------------------------------------- 
mtz_file= None MTZ file containing map coefficients
pdb_file= None Model file around which to draw the map. If not supplied, the
          map will fill the unit cell.
labels= None Map column labels. Common examples are 2FOFCWT,PH2FOFCWT and
        FP,SIGFP PHIM FOMM . If left blank, all maps present in the input file
        will be used.
buffer= 5.0 Extra padding (in Angstroms) around the selected region (or unit
        cell)
selection= None Atom selection around which to draw map (plus buffer). If left
           blank, the entire model file will be used.
d_min= None High-resolution cutoff
d_max= None Low-resolution cutoff
grid_resolution_factor= 1.0 / 3 Grid spacing (multiplied by the
                        high-resolution limit)
scale= *sigma volume Scaling method for map values
include_fmodel= False
show_maps= False
output
   directory= None Output directory (defaults to current)
   prefix= None Output file prefix (defaults to the MTZ file name base)
   job_title= None Job title in PHENIX GUI, not used on command line
   format= xplor *ccp4
   extension= *Auto ccp4 xplor map
r_free_flags
   remove= False
   file_name= None
   label= None
   test_flag_value= None