The real thing : keyworded input.

The core of GraphEnt understands nothing of AUTO-labelled files, or even worse, .mtz files. What is really happening, is that when a .mtz file is specified on input, a function is called which prepares an AUTO-labeled ASCII file (with the name MAXENT_FROM_MTZ.in which is left behind after the program is finished). But, again, the core of GraphEnt can not interprete the AUTO flag. So, another function is called which translates the AUTO-labeled file to a keyworded format that GraphEnt can understand¹⁴, like this one :

CELL               94.14900        24.17000        64.31901        90.00000       130.36700        90.00000
SPACEGROUP   1
VERBOSE
GRACYCLES    20
GRATWOWINDOWS
MAP_FORMAT   CCP4
DIFF_PATT
PERMUTATION  3 1 2
GRID            128    128      1
REFLECTIONS
   -22     0     6          50.32293         2.43270        67.66310         2.33278
   -22     0     7         148.78082         3.24875       139.47423         2.21939
   -22     0     8         189.90724         3.95280       210.31883         2.26664
   .................................................................................
    14     0     3         250.23837         4.61909       307.68475         4.29308
    16     0     0         760.94031        15.55367       687.91992         8.57631
    16     0     1         350.09189         6.37660       328.42670         3.76660

No matter what the name of your .mtz or AUTO-labelled file is, the input file for the GraphEnt calculation is called MAXENT_AUTO.IN and is left behind after the calculation is finished. Needless to say that you can prepare or edit such a file and give it to GraphEnt by typing GraphEnt <my_file.in> (but, again, you can not specify resolution limits or projections if you run the program this way).

Although you will probably stick to using one or the other wrapper, there are situations where editing and using the keyworded input file is neccessary. Examples include the following : increasing the grid size (because you are getting splitted peaks for example), changing the axes permutation, excluding reflections from the calculation, selecting which map section to plot, and whether or not to use a grayscale plus contour representation, reducing the amount of output from the program, etc.

Comments can be incorporated in the file (but not after the REFLection keyword) by starting the comment line with a !, # or an asterisk ( *). Please also note that the keywords are recognised using only the first four characters. A detailed description of the various keywords follows :

NOTE : The default (expected) reflection structure for GraphEnt is to read h, k, l,| F|,(| F|), for each reflection record. This default is modified by the keywords PATT, DIFF and FOM. If none of these keywords is present, then you are expected to define six (and only six) columns for the reflection records containing h, k, l,| F|,(| F|) and , even if what you are calculating is not a phased synthesis (to make it clear, if you are calculating a Patterson function, you would have to have a last column containing zeros).

Footnotes

... understand¹⁴

In other words, .mtz files are going through two translation stages, and AUTO-labelled files through one.