Difference between revisions of "Cppxfel Statistics"

Revision as of 17:23, 25 November 2015

There are a number of merging statistics and plots which can be generated using cppxfel and your favourite graph-drawing software. cppxfel has a number of commands which generate CSV files which can be plotted elsewhere.

Correlation between two images

cppxfel can be used to generate plots of intensities between two images. To calculate the correlation between two halves of the data set in the first merge:

cppxfel.run -cc half1Merge0.mtz half2Merge0.mtz

This creates a new CSV file named correlation.csv. This can also be carried out for individual images:

cppxfel.run -cc allMerge5.mtz ref-img-shot-s00-20130316165414164_0.mtz

The beginning of correlation.csv begins as so. The "first intensity" and "second intensity" columns can be plotted in a suitable program (e.g. R, Veusz, etc.).

<pre>
h k l,First intensity,Second intensity,Resolution
0 1 29,6788.76,6681.7,3.64553
0 1 49,113.671,234.905,2.15839
0 1 53,24.636,44.4067,1.99555
0 1 57,110.308,175.868,1.85556
0 2 4,346.637,351.928,23.6538
0 2 18,11660.6,11678.3,5.8409
0 2 36,143.598,30.5506,2.9339
0 2 42,1503.52,1370.33,2.5158
0 2 50,29.0206,20.7457,2.11397
0 2 52,59.3656,110.755,2.03279
0 3 5,5267.67,5281.37,18.1417
0 3 15,786.865,2939.76,6.91526
0 3 47,82.9657,111.247,2.24614
0 3 49,218.114,361.618,2.15481
0 4 16,130.598,202.681,6.41405
0 4 34,9586.69,8670.65,3.08996
0 4 42,619.911,235.344,2.5073
0 4 44,3396.41,3825.67,2.39429
0 4 50,661.039,709.513,2.10893

Partiality plot for an individual image

cppxfel can produce a CSV file containing information on the success of the partiality model for a particular image. This requires a reference MTZ (generated with > 2.0-3.0 multiplicity) and an image of the format ref-img*.mtz created by the standard input file refine.txt.

This can be generated as follows:

cppxfel.run -partiality allMerge5.mtz ref-img-shot-s00-20130316165414164_0.mtz

Alternatively, a maximum resolution can be specified:

cppxfel.run -partiality allMerge5.mtz ref-img-shot-s00-20130316165414164_0.mtz 2.0

This creates the following output on the screen:

Running cppxfel...
Welcome to cppxfel!
 SYMINFO file set to /apps/strubi/ccp4/ccp4-6.5/lib/data/syminfo.lib 
Loaded 23822 reflections (23822 accepted).
Setting reference to allMerge5.mtz
Partiality plot for ref-img-shot-s00-20130316165414164_0.mtz
 SYMINFO file set to /apps/strubi/ccp4/ccp4-6.5/lib/data/syminfo.lib 
Loaded 3002 reflections (3002 accepted).
Ambiguity 0: 0.622248, ambiguity 1: 0.931926
2754 reflections in common with reference MTZ.
Total number of reflections in MTZ: 2890
     Low res    High res   Num refl.
         inf     2.53984         718
     2.53984     2.01587        1100
     2.01587     1.76103         879
     1.76103         1.6         167
N: Total time: 0 minutes, 1 seconds (1 seconds).
Done

This shows the four resolution bins used to generate the data, and outputs the appropriate data to partiality_[n].csv where [n] is the number of generated bins. The format of the partiality CSV files is as follows:

h,k,l,wavelength,partiality,percentage,intensity,resolution
4,2,-6,1.37061,0,3.76223,263.63,0.070742
2,2,-4,1.39565,0.419087,20.8099,142.831,0.0463115
-9,4,9,1.4039,0,3.41021,24.9747,0.126123
-1,9,-6,1.41084,0,3.08305,35.6135,0.102689
3,20,-15,1.41234,0,2.05453,94.6172,0.238028
-10,28,-4,1.41258,0,96.443,158.223,0.283599
17,24,-25,1.41401,0,94.9401,74.3205,0.364902
18,-6,-10,1.41447,0,0.439069,56.5138,0.202751
11,25,-22,1.41478,0,1.55951,39.9897,0.33154
-15,35,2,1.41483,0,1.32867,9.05428,0.360467
-19,8,35,1.41484,0,0,-1.88631,0.383995
-17,4,35,1.41519,0,35.4585,59.3055,0.369768

The wavelength column corresponds to the Ewald sphere on which the centre of the reciprocal lattice point is found in Å, the partiality column is the theoretically calculated partiality value, the percentage column is the percentage (intensity for a given image / intensity of reference data set), the intensity is the raw integrated intensity for that reflection and the resolution is d* or 1 / d, in Å^-1.

One should plot the wavelength on the X axis and both the partiality and percentage columns on separate Y axes, and one hopes that the partiality and percentage graphs match each other as closely as possible.