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 Testing the executable

Assuming that the executable is in your PATH, and that its name is GraphEnt, go to the /my_dirs/GraphEnt/examples/ directory, make your window at least 125 characters wide, and type GraphEnt Myoglobin_anom_Patt.in. What you should see on your terminal should be similar to this :


___________________________________________________________________________________________________________________________
                                                                                    
                              ###   ###                   #######            #      
                               ##   ##                     #    #            #      
                               # # # #   ####   ### ###    #    # ## ###   ######   
                               # # # #  #    #   #   #     #  #    ##   #    #      
                               #  #  #       #    # #      ####    #    #    #      
                               #  #  #   #####     #       #  #    #    #    #      
                               #     #  #    #    # #      #    #  #    #    #      
                               #     #  #    #   #   #     #    #  #    #    #   #  
                              ###   ###  #### # ### ###   ####### ###  ###    ###   
                                                                                            
                            Gull, S.F. & Daniell, G.J. (1978), Nature, 272, 686-690         
                                   Collins, D.M. (1982), Nature, 298, 49-51                 
                                                                                            
                                                      NMG                                   
                                                                                                
___________________________________________________________________________________________________________________________

Keyword             CELL : Cell dimensions set to  35.84  28.89  63.57  90.00 105.47  90.00
Keyword         GRAFIRST : first contour at mean + 1.000000 rmsd.
Keyword         GRALEVEL : contouring interval set to 1.000000 rmsd.
Keyword           TARGET : target value for chi^2 set to 100.00
Keyword           LAMBDA : initial value for lambda set to 40000.000000
Keyword          VERBOSE : verbose mode set.
Keyword       GRASECTION : Plot section 28.
Keyword            LIMIT : exclude reflections with |F|/sig(|F|)<0.500000.
Keyword       SPACEGROUP : space group number set to 1
Keyword       MAP_FORMAT : CCP4 map file selected.
Keyword        PATTERSON : Patterson map run [h k l F sig(F)].
Keyword      PERMUTATION : Permutation set to 3 1 2
Keyword             GRID : Grid set to   160    96    56
Keyword        GRACYCLES : Plot every 5 cycles.
Keyword    GRATWOWINDOWS : Will keep conventional map plot.
Keyword      REFLECTIONS : start reading reflections.
2274 reflections rejected due to sigma cutoff (Keyword LIMIt)
___________________________________________________________________________________________________________________________

   Added reflection   -2   +6   +0        +42.336       +40.730     +0.0 
   Added reflection   -2   -6   +0        +42.336       +40.730     +0.0 
   Added reflection   -3   +8   +0       +229.620      +406.417     +0.0 
   Added reflection   -3   +7   +0        +23.072       +45.970     +0.0 
   Added reflection   -3   -7   +0        +23.072       +45.970     +0.0 
   Added reflection   -3   -8   +0       +229.620      +406.417     +0.0 
   Added reflection   -4   +7   +0       +341.880      +424.920     +0.0 
   Added reflection   -4   +6   +0       +152.727      +194.618     +0.0 
   Added reflection   -4   -6   +0       +152.727      +194.618     +0.0 
   Added reflection   -4   -7   +0       +341.880      +424.920     +0.0 
   Added reflection   -5   +6   +0        +37.322       +72.535     +0.0 
   Added reflection   -5   -6   +0        +37.322       +72.535     +0.0 
   Added reflection   -8   +6   +0        +64.509       +93.693     +0.0 
   Added reflection   -8   -6   +0        +64.509       +93.693     +0.0 
   Added reflection  -10   +4   +0       +113.128      +167.607     +0.0 
   Added reflection  -10   -4   +0       +113.128      +167.607     +0.0 

 - F000 not given. Set to 3793.957764
 - Initial lambda is 40000.000
 - Verbose output requested.
 - Lambda linearly depended on number of cycles.
 - Grid (along fast, medium and slow)   160     96     56
 - Axes permutation is fast-Z, medium-X, slow-Y 


 - About to allocate memory.                                  
 - FFTW is learning how to do FFTs  ...  
 - FFTW learned how to do FFTs.    
 - Saving FFTW's wisdom file ...    
     There are 636 observations with <F>=    140.28                  
 - Loading data on arrays ...                                 
 - Do not panic yet ...  
 - About to calculate conventional Fourier transform of data   
 - Write out conventional Fourier transform (file conventional.map)
 - Sum and average of densities are     -19.6406 and       0.0000.
 - Scale factor applied :      0.00574329.
 - Map entropy is undefined (negative values are present).
<!--SUMMARY_BEGIN-->
  (Q)QOPEN allocated #  1
 User:   glykos               Logical Name: conventional.map
 Status: UNKNOWN    Filename: conventional.map
<!--SUMMARY_END-->

  File name for output map file on unit   1 : conventional.map
     logical name conventional.map


 FORMATTED      OLD     file opened on unit  24
 Logical name: SYMOP, Full name: /disk2/public/xtal/ccp4/lib/data/symop.lib


   Minimum density in map  =     -262.72626   Maximum density         =      999.00000
   Mean density            =        0.00000
   Rms deviation from mean =       58.00461




___________________________________________________________________________________________________________________________

 - MAXENT starts here                                   


 Chi**2 :         492.602     R : 1.0000       Lambda :  40000.00000       Nobs :     618 
 Chi**2 :         463.573     R : 0.9882       Lambda :  40000.00000       Nobs :     618 
 Chi**2 :         438.420     R : 0.9766       Lambda :  40800.00000       Nobs :     618 
 Chi**2 :         415.155     R : 0.9648       Lambda :  41616.00000       Nobs :     618 
 Chi**2 :         393.011     R : 0.9524       Lambda :  42448.32000       Nobs :     618 
 Chi**2 :         371.457     R : 0.9393       Lambda :  43297.28640       Nobs :     618 
 Chi**2 :         350.097     R : 0.9250       Lambda :  44163.23213       Nobs :     618 
 Chi**2 :         328.631     R : 0.9095       Lambda :  45046.49677       Nobs :     618 
 Chi**2 :         306.893     R : 0.8923       Lambda :  45947.42671       Nobs :     618 
 Chi**2 :         284.879     R : 0.8732       Lambda :  46866.37524       Nobs :     618 
 Chi**2 :         262.809     R : 0.8524       Lambda :  47803.70274       Nobs :     618 
 Chi**2 :         241.128     R : 0.8302       Lambda :  48759.77680       Nobs :     618 
 Chi**2 :         220.455     R : 0.8074       Lambda :  49734.97234       Nobs :     618 
 Chi**2 :         201.431     R : 0.7845       Lambda :  50729.67178       Nobs :     618 
 Chi**2 :         184.532     R : 0.7620       Lambda :  51744.26522       Nobs :     618 
 Chi**2 :         169.935     R : 0.7411       Lambda :  52779.15052       Nobs :     618 
 Chi**2 :         157.517     R : 0.7220       Lambda :  53834.73353       Nobs :     618 
 Chi**2 :         146.969     R : 0.7051       Lambda :  54911.42820       Nobs :     618 
 Chi**2 :         137.930     R : 0.6903       Lambda :  56009.65677       Nobs :     618 
 Chi**2 :         130.084     R : 0.6769       Lambda :  57129.84990       Nobs :     618 
 Chi**2 :         123.181     R : 0.6647       Lambda :  58272.44690       Nobs :     618 
 Chi**2 :         117.044     R : 0.6535       Lambda :  59437.89584       Nobs :     618 
 Chi**2 :         111.535     R : 0.6435       Lambda :  60626.65376       Nobs :     618 
 Chi**2 :         106.558     R : 0.6343       Lambda :  61839.18683       Nobs :     618 
 Chi**2 :         102.034     R : 0.6261       Lambda :  63075.97057       Nobs :     618 
 Chi**2 :          97.914     R : 0.6181       Lambda :  64337.48998       Nobs :     618 

 Chi**2 :          97.914     R : 0.6181       Lambda :  64337.48998       Nobs :     618 
 25 cycles in 74 seconds, giving an average of 2.960 seconds per cycle.
___________________________________________________________________________________________________________________________



CONVERGENCE ACHIEVED.
The final R-factor between the observed
and calculated amplitudes is  0.6180865 


 - Write out maxent.map map file.                                     
 - Sum and average of densities are    3953.8928 and       0.0046.
 - Scale factor applied :    374.67059326.

 - Map entropy is 13.583438.
 (Q)QOPEN status changed from NEW to UNKNOWN for maxent.map
<!--SUMMARY_BEGIN-->
  (Q)QOPEN allocated #  1
 User:   glykos               Logical Name: maxent.map
 Status: UNKNOWN    Filename: maxent.map
<!--SUMMARY_END-->

  File name for output map file on unit   1 : maxent.map
     logical name maxent.map


 FORMATTED      OLD     file opened on unit  24
 Logical name: SYMOP, Full name: /disk2/public/xtal/ccp4/lib/data/symop.lib


   Minimum density in map  =        0.09199   Maximum density         =      999.00006
   Mean density            =        1.72224
   Rms deviation from mean =        2.78240




 - Calculating table of largest contributions to chi**2
 - Will write out all reflections contributing to chi^2 by more than 10.000000 times the rmsd of all contributions.



Normal termination ? (82 seconds)

At this point, and if you have graphics support, you should also have three graphics windows on your monitor, one on top of the other (but you can move them of course). Hit <RETURN> in the terminal window to finish with the run and close the graphics windows.

If you went into the trouble of looking at the sections plotted in the graphics windows, you would be forgiven to think that something is wrong (``Ooops. The maxent map has an origin peak at the middle of nowhere.''). Actually, the peak in the GraphEnt map is the Fe-Fe anomalous Patterson peak. It is not present in the conventional map due to the presence of three outliers in the data. If you do not take my word for it, do a diff Myoglobin_anom_Patt.in Myoglobin_anom_Patt_no_outliers.in, and then type GraphEnt Myoglobin_anom_Patt_no_outliers.in to confirm for yourself that after the removal of the outliers, this peak is the strongest feature in the conventional map as well (this example is discussed in more detail in GraphEnt's paper).

If your executable does not support graphics (and if it is a DEC Alpha 1200), you should see something like :


___________________________________________________________________________________________________________________________
                                                                                    
                              ###   ###                   #######            #      
                               ##   ##                     #    #            #      
                               # # # #   ####   ### ###    #    # ## ###   ######   
                               # # # #  #    #   #   #     #  #    ##   #    #      
                               #  #  #       #    # #      ####    #    #    #      
                               #  #  #   #####     #       #  #    #    #    #      
                               #     #  #    #    # #      #    #  #    #    #      
                               #     #  #    #   #   #     #    #  #    #    #   #  
                              ###   ###  #### # ### ###   ####### ###  ###    ###   
                                                                                            
                            Gull, S.F. & Daniell, G.J. (1978), Nature, 272, 686-690         
                                   Collins, D.M. (1982), Nature, 298, 49-51                 
                                                                                            
                                                      NMG                                   
                                                                                                
___________________________________________________________________________________________________________________________

Keyword             CELL : Cell dimensions set to  35.84  28.89  63.57  90.00 105.47  90.00
Keyword         GRAFIRST given, but PGPLOT not defined.
Keyword         GRALEVEL given, but PGPLOT not defined.
Keyword           TARGET : target value for chi^2 set to 100.00
Keyword           LAMBDA : initial value for lambda set to 40000.000000
Keyword          VERBOSE : verbose mode set.
Keyword       GRASECTION given, but PGPLOT not defined.
Keyword            LIMIT : exclude reflections with |F|/sig(|F|)<0.500000.
Keyword       SPACEGROUP : space group number set to 1
CCP4 map selected, but program compiled without CCP4 support. na4 set.
Keyword        PATTERSON : Patterson map run [h k l F sig(F)].
Keyword      PERMUTATION : Permutation set to 3 1 2
Keyword             GRID : Grid set to   160    96    56
Keyword        GRACYCLES given, but PGPLOT not defined.
Keyword    GRATWOWINDOWS given, but PGPLOT not defined.
Keyword      REFLECTIONS : start reading reflections.
2274 reflections rejected due to sigma cutoff (Keyword LIMIt)
___________________________________________________________________________________________________________________________

   Added reflection   -2   +6   +0        +42.336       +40.730     -0.0 
   Added reflection   -2   -6   +0        +42.336       +40.730     -0.0 
   Added reflection   -3   +8   +0       +229.620      +406.417     -0.0 
   Added reflection   -3   +7   +0        +23.072       +45.970     -0.0 
   Added reflection   -3   -7   +0        +23.072       +45.970     -0.0 
   Added reflection   -3   -8   +0       +229.620      +406.417     -0.0 
   Added reflection   -4   +7   +0       +341.880      +424.920     -0.0 
   Added reflection   -4   +6   +0       +152.727      +194.618     -0.0 
   Added reflection   -4   -6   +0       +152.727      +194.618     -0.0 
   Added reflection   -4   -7   +0       +341.880      +424.920     -0.0 
   Added reflection   -5   +6   +0        +37.322       +72.535     -0.0 
   Added reflection   -5   -6   +0        +37.322       +72.535     -0.0 
   Added reflection   -8   +6   +0        +64.509       +93.693     -0.0 
   Added reflection   -8   -6   +0        +64.509       +93.693     -0.0 
   Added reflection  -10   +4   +0       +113.128      +167.607     -0.0 
   Added reflection  -10   -4   +0       +113.128      +167.607     -0.0 

 - F000 not given. Set to 3793.957764
 - Initial lambda is 40000.000
 - Verbose output requested.
 - Lambda linearly depended on number of cycles.
 - Grid (along fast, medium and slow)   160     96     56
 - Axes permutation is fast-Z, medium-X, slow-Y 


 - About to allocate memory.                                  
 - FFTW is learning how to do FFTs  ...  
 - FFTW learned how to do FFTs.    
 - Saving FFTW's wisdom file ...    
     There are 636 observations with <F>=    140.28                  
 - Loading data on arrays ...                                 
 - Do not panic yet ...  
 - About to calculate conventional Fourier transform of data   
 - Write out conventional Fourier transform (file conventional.map)
 - Sum and average of densities are     -19.3750 and      -0.0000.
 - Scale factor applied :      0.00574329.
 - Map entropy is undefined (negative values are present).



___________________________________________________________________________________________________________________________

 - MAXENT starts here                                   


 Chi**2 :         492.602     R : 1.0000       Lambda :  40000.00000       Nobs :     618 
 Chi**2 :         463.573     R : 0.9882       Lambda :  40000.00000       Nobs :     618 
 Chi**2 :         438.420     R : 0.9766       Lambda :  40800.00000       Nobs :     618 
 Chi**2 :         415.155     R : 0.9648       Lambda :  41616.00000       Nobs :     618 
 Chi**2 :         393.011     R : 0.9524       Lambda :  42448.32000       Nobs :     618 
 Chi**2 :         371.457     R : 0.9393       Lambda :  43297.28640       Nobs :     618 
 Chi**2 :         350.097     R : 0.9250       Lambda :  44163.23213       Nobs :     618 
 Chi**2 :         328.631     R : 0.9095       Lambda :  45046.49677       Nobs :     618 
 Chi**2 :         306.893     R : 0.8923       Lambda :  45947.42671       Nobs :     618 
 Chi**2 :         284.879     R : 0.8732       Lambda :  46866.37524       Nobs :     618 
 Chi**2 :         262.809     R : 0.8524       Lambda :  47803.70274       Nobs :     618 
 Chi**2 :         241.128     R : 0.8302       Lambda :  48759.77680       Nobs :     618 
 Chi**2 :         220.455     R : 0.8074       Lambda :  49734.97234       Nobs :     618 
 Chi**2 :         201.431     R : 0.7845       Lambda :  50729.67178       Nobs :     618 
 Chi**2 :         184.532     R : 0.7620       Lambda :  51744.26522       Nobs :     618 
 Chi**2 :         169.935     R : 0.7411       Lambda :  52779.15052       Nobs :     618 
 Chi**2 :         157.517     R : 0.7220       Lambda :  53834.73353       Nobs :     618 
 Chi**2 :         146.969     R : 0.7051       Lambda :  54911.42820       Nobs :     618 
 Chi**2 :         137.930     R : 0.6903       Lambda :  56009.65677       Nobs :     618 
 Chi**2 :         130.083     R : 0.6769       Lambda :  57129.84990       Nobs :     618 
 Chi**2 :         123.181     R : 0.6647       Lambda :  58272.44690       Nobs :     618 
 Chi**2 :         117.044     R : 0.6535       Lambda :  59437.89584       Nobs :     618 
 Chi**2 :         111.535     R : 0.6435       Lambda :  60626.65376       Nobs :     618 
 Chi**2 :         106.558     R : 0.6343       Lambda :  61839.18683       Nobs :     618 
 Chi**2 :         102.034     R : 0.6261       Lambda :  63075.97057       Nobs :     618 
 Chi**2 :          97.914     R : 0.6181       Lambda :  64337.48998       Nobs :     618 

 Chi**2 :          97.914     R : 0.6181       Lambda :  64337.48998       Nobs :     618 
 25 cycles in 16 seconds, giving an average of 0.640 seconds per cycle.
___________________________________________________________________________________________________________________________



CONVERGENCE ACHIEVED.
The final R-factor between the observed
and calculated amplitudes is  0.6180865 


 - Write out maxent.map map file.                                     
 - Sum and average of densities are    3953.9036 and       0.0046.
 - Scale factor applied :    374.67068481.
 - Map entropy is 13.583428.



 - Calculating table of largest contributions to chi**2
 - Will write out all reflections contributing to chi^2 by more than 10.000000 times the rmsd of all contributions.



Normal termination ? (20 seconds)

and the program will not wait for input. Note that the exect numerical results you are getting depend on your computer's hardware and the compiler flags used, and so, you should not be expecting to see exactly the numbers shown in the examples above.


next up previous contents
Next:  Supported crystallographic calculations Up:  Installation guide Previous:  Building from source   Contents
NMG, March 2000