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.