Program output

Depending on the type of calculation performed, GraphEnt can create up to four graphics windows and leave behind (after the calculation is over) up to 10 files. The number of files created depends not only on the type of calculation performed but also on the availability of PGPLOT with your executable¹¹.

The four possible graphics windows are :

1. A window showing a section from the conventional Fourier syntesis (the section plotted can be selected with the keyword GRASection, see page ).
2. A window showing the same section from the MaxEnt map.
3. A normal probability plot of the input data (calculated only in the case of a difference Patterson calculation).
4. A scatter plot of the contribution of each reflection to the final value of .

A directory devoted to running GraphEnt may contain all these files after the end of the calculation (assuming that you started with just the file myfile.mtz) :

total 2440
-rw-r--r--   1 glykos    sys           68 Mar 27 18:19 CHIcontributions.dat
-rw-r--r--   1 glykos    sys        39223 Mar 27 18:19 CHIcontributions.ps
-rw-r--r--   1 glykos    sys        63767 Mar 27 18:14 CONVENTIONAL.ps
-rw-r--r--   1 glykos    sys        65022 Mar 27 18:18 GRAPHENT.ps
-rw-r--r--   1 glykos    sys        75097 Mar 27 18:14 MAXENT_AUTO.IN
-rw-r--r--   1 glykos    sys        73771 Mar 27 18:14 MAXENT_FROM_MTZ.in
-rw-r--r--   1 glykos    sys        38583 Mar 27 18:14 MAXENT_FROM_MTZ_ANOMALOUS.in
-rw-r--r--   1 glykos    sys        50092 Mar 27 18:14 MAXENT_SUM_PATT.in
-rw-r--r--   1 glykos    sys        16754 Mar 27 18:14 Normal_probability.ps
-rw-r--r--   1 glykos    sys         3740 Mar 27 18:14 Normplot_tails.dat
-rw-r--r--   1 glykos    sys       861264 Mar 27 18:14 conventional.map
-rw-r--r--   1 glykos    sys       861264 Mar 27 18:18 maxent.map
-rw-r--r--   1 glykos    sys       317920 Mar 27 18:14 myfile.mtz

The file myfile.mtz is where you started from, and the files conventional.map and maxent.map are the conventional and maxent map files containing the syntheses corresponding to your data (see below for a description of the supported map formats).

The files CONVENTIONAL.ps and GRAPHENT.ps are only produced if you have graphics support and contain postscript images of the conventional and GraphEnt map sections that were plotted on your monitor.

The files Normal_probability.ps and Normplot_tails.dat are produced only when you are performing a difference Patterson calculation. See page  for a more detailed discussion of the normal probability plot facility.

The file CHIcontributions.ps is only produced if you have graphics support and it contains the contribution of each reflection to the final value of . The ASCII file CHIcontributions.dat contains a list of reflections whose contribution to is higher than 10 above the mean contribution of all reflections. Depending on the case, these reflections may also be flagged as ``suspect'' (the 10 limit can be changed with the keyword CHILimit, page ). In conjunction with the keyword REJEct, some or all of these reflections can be excluded from a subsequent calculation (page ).

Finally, the files that start with MAXENT_ are intermediate files produced during the interpretation of the .mtz file, or, in the case of MAXENT_FROM_MTZ_ANOMALOUS.in and MAXENT_SUM_PATT.in, files that can be used as input to GraphEnt for calculating an anomalous differences Patterson function, and a so-called ``summed'' difference Patterson (based on F_H ). Please note that I have not used the MAXENT_SUM_PATT.in file extensively, so there might as well be some bugs lurking in there.

Footnotes

... executable¹¹

The reason is that with PGPLOT it is relatively easy to save the contents of a graphics window as a postscript file. GraphEnt is using this facility to save postscript versions of the normal probability plot and of the graph showing the contributions of each reflection to .