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 :
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
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).