Overview

GraphEnt is an attempt to provide an automatic way for calculating the maximum entropy map that corresponds to a set of observations, while offering a useful graphical output of the current stage of the calculations. Here is a screenshot from a SGI workstation running GraphEnt :

Figure: Screenshot

The automation is mainly directed towards the macromolecular crystallographic community, with direct support for CCP4 mtz reflection files. Doing the calculation is as simple as graphent 15 3.5 my_file.mtz (for a GUI-based selection of the type of synthesis you want to calculate), GraphEnt 15 4 my_file.mtz (for a fully automated run using all data between 15 and 4Å resolution), or GraphEnt h0l 10.0 3.5 my_file.mtz (for calculating the GraphEnt map corresponding to the [010] projection using only data between 10.0 and 3.5Å resolution).

Having said that, it is still quite easy for the general crystallographic community to use the program. All is needed is an ASCII file containing unit cell dimensions and a list of reflections expanded to P1 :

                 AUTO  30.40 42.10 81.40 90.00 90.00 90.00  20
                   -7  -5   1  559.200    8.700  138.578  0.4500
                 ...............................................
                    8   0   0  415.500    9.500  180.000  0.4000

Clearly, this black-box approach leads to loss of flexibility¹. For this reason, GraphEnt also supports a more detailed form of input files, like this one² :

                 CELL            30.40 42.10 81.40 90.00 90.00 90.00
                 SPACEGROUP      20                                 
                 GRID            128 64 64                          
                 PERM            3 1 2                              
                 FOM                                                
                 VERBOSE                                            
                 GRACYCLES       5                                  
                 GRASECTION      14                                 
                 GRAGRAYSCALE                                       
                 LAMBDA          1.0                                
                 MAP_FORMAT      ccp4                               
                 REFL                                               
                   -7  -5   1  559.200    8.700  138.578  0.4500    
                   -7  -5   2  276.600   11.400  220.410  0.3500    
                  ...............................................    
                    7   5   3  532.700    8.900  349.320  0.4400    
                    8   0   0  415.500    9.500  180.000  0.4000

This document is organised as follows : Section 4 is for the impatient who just want to give it a try (and hopefully not get what they deserve). Section 5 gives a quick overview of the algorithm and a pictorial introduction to the advantages of the method. Section 6.1 discusses how to install and test the program. Sections 6.2, 6.3 and 6.4 present the supported modes of operation and the automated modes of execution. Section 6.5 presents the files produced by GraphEnt, and section 6.7 discusses the use of the normal probability plot produced by the program. Finally, section 7 contains the list of keywords recognised by GraphEnt.

Footnotes

... flexibility¹

For example, this input file with 7 columns of which the last one is always less or equal to 1.0, will be interpreted by GraphEnt as a request for a phased figure-of-merit-weighted Fourier synthesis, and there is very little you can do to change this in the automatic mode.

... one²

Actually, GraphEnt only understands this detailed form of input. The automatic modes are wrappers which prepare an input file that the core program can interpret.