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 :
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## ## # # #
# # # # #### ### ### # # ## ### ######
# # # # # # # # # # ## # #
# # # # # # #### # # #
# # # ##### # # # # # #
# # # # # # # # # # #
# # # # # # # # # # # #
### ### #### # ### ### ####### ### ### ###
Beta, Release 1.1
Gull, S.F. & Daniell, G.J. (1978), Nature, 272, 686-690
Collins, D.M. (1982), Nature, 298, 49-51
NMG
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Keyword CELL : Cell dimensions set to 35.84 28.89 63.57 90.00 105.47 90.00
Keyword F000 : F000 known and set to 30.000000.
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 0.500000 (fractional coordinates).
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)
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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
- Square F000 for Patterson calculation, F000=900.000000.
- 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
- Data structures require 19.9 MBytes of memory.
- 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 -19.0625 and -0.0000.
- Scale factor applied : 0.00574329.
- Map entropy is undefined (negative values are present).
(Q)QOPEN: file opened on unit 1 Status: UNKNOWN
Logical Name: conventional.map Filename: conventional.map
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, Filename: /usr/local/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
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- MAXENT starts here
Chi**2 : 492.602 R : 1.0000 Lambda : 40000.00000 Nobs : 620
Chi**2 : 485.034 R : 0.9972 Lambda : 40000.00000 Nobs : 620
Chi**2 : 477.884 R : 0.9942 Lambda : 40800.00000 Nobs : 620
Chi**2 : 470.680 R : 0.9911 Lambda : 41616.00000 Nobs : 620
Chi**2 : 463.181 R : 0.9877 Lambda : 42448.32000 Nobs : 620
Chi**2 : 455.133 R : 0.9837 Lambda : 43297.28640 Nobs : 620
Chi**2 : 446.211 R : 0.9791 Lambda : 44163.23213 Nobs : 620
Chi**2 : 435.969 R : 0.9735 Lambda : 45046.49677 Nobs : 620
Chi**2 : 423.800 R : 0.9663 Lambda : 45947.42671 Nobs : 620
Chi**2 : 408.912 R : 0.9568 Lambda : 46866.37524 Nobs : 620
Chi**2 : 390.377 R : 0.9441 Lambda : 47803.70274 Nobs : 620
Chi**2 : 367.352 R : 0.9270 Lambda : 48759.77680 Nobs : 620
Chi**2 : 339.573 R : 0.9045 Lambda : 49734.97234 Nobs : 620
Chi**2 : 308.114 R : 0.8762 Lambda : 50729.67178 Nobs : 620
Chi**2 : 275.884 R : 0.8436 Lambda : 51744.26522 Nobs : 620
Chi**2 : 246.902 R : 0.8105 Lambda : 52779.15052 Nobs : 620
Chi**2 : 224.139 R : 0.7802 Lambda : 53834.73353 Nobs : 620
Chi**2 : 207.880 R : 0.7553 Lambda : 54911.42820 Nobs : 620
Chi**2 : 196.440 R : 0.7363 Lambda : 56009.65677 Nobs : 620
Chi**2 : 187.910 R : 0.7225 Lambda : 57129.84990 Nobs : 620
Chi**2 : 181.006 R : 0.7118 Lambda : 58272.44690 Nobs : 620
Chi**2 : 175.019 R : 0.7033 Lambda : 59437.89584 Nobs : 620
Chi**2 : 169.590 R : 0.6960 Lambda : 60626.65376 Nobs : 620
Chi**2 : 164.540 R : 0.6897 Lambda : 61839.18683 Nobs : 620
Chi**2 : 159.778 R : 0.6839 Lambda : 63075.97057 Nobs : 620
Chi**2 : 155.255 R : 0.6784 Lambda : 64337.48998 Nobs : 620
Chi**2 : 150.940 R : 0.6732 Lambda : 65624.23978 Nobs : 620
Chi**2 : 146.815 R : 0.6682 Lambda : 66936.72457 Nobs : 620
Chi**2 : 142.864 R : 0.6634 Lambda : 68275.45907 Nobs : 620
Chi**2 : 139.076 R : 0.6586 Lambda : 69640.96825 Nobs : 620
Chi**2 : 135.441 R : 0.6540 Lambda : 71033.78761 Nobs : 620
Chi**2 : 131.950 R : 0.6494 Lambda : 72454.46336 Nobs : 620
Chi**2 : 128.597 R : 0.6450 Lambda : 73903.55263 Nobs : 620
Chi**2 : 125.375 R : 0.6406 Lambda : 75381.62368 Nobs : 620
Chi**2 : 122.279 R : 0.6363 Lambda : 76889.25616 Nobs : 620
Chi**2 : 119.304 R : 0.6321 Lambda : 78427.04128 Nobs : 620
Chi**2 : 116.444 R : 0.6279 Lambda : 79995.58211 Nobs : 620
Chi**2 : 113.695 R : 0.6239 Lambda : 81595.49375 Nobs : 620
Chi**2 : 111.051 R : 0.6200 Lambda : 83227.40362 Nobs : 620
Chi**2 : 108.508 R : 0.6161 Lambda : 84891.95170 Nobs : 620
Chi**2 : 106.060 R : 0.6122 Lambda : 86589.79073 Nobs : 620
Chi**2 : 103.702 R : 0.6084 Lambda : 88321.58654 Nobs : 620
Chi**2 : 101.429 R : 0.6047 Lambda : 90088.01828 Nobs : 620
Chi**2 : 99.237 R : 0.6010 Lambda : 91889.77864 Nobs : 620
Chi**2 : 99.237 R : 0.6010 Lambda : 91889.77864 Nobs : 620
43 cycles in 36 seconds, giving an average of 0.837 seconds per cycle.
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CONVERGENCE ACHIEVED.
The final R-factor between the observed
and calculated amplitudes is 0.6010417
- Write out maxent.map map file.
- Sum and average of densities are 1101.5133 and 0.0013.
- Scale factor applied : 173.43777466.
- Map entropy is 13.157804.
(Q)QOPEN status changed from NEW to UNKNOWN for maxent.map
(Q)QOPEN: file opened on unit 1 Status: UNKNOWN
Logical Name: maxent.map Filename: maxent.map
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, Filename: /usr/local/ccp4/lib/data/symop.lib
Minimum density in map = 0.00242 Maximum density = 998.99994
Mean density = 0.22210
Rms deviation from mean = 2.12448
- 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 ? (45 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.
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 example above.