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CCP4i: Graphical User Interface |
| Tutorial 4 |
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The correlation coefficients and Rfactors as they came out of the simple AMoRe example are not particularly promising. It is, therefore, wise to play around with some of the parameters.
Do not worry about the jumping of windows. Whenever only a shape of a window comes up, position it on the screen where you want it (as before).
The Interface calculates an optimal size and shape for the model cell (see AMoRe Rotation Function Radius and Model Cell): 91.146 61.096 61.406 in this case. Opinions differ as to the values to use (see AMoRe Program Documentation). The Interface uses Navaza's method.
The parameters to change in the Interface, are
Model cell x, y and z in the 'Rotation Function Parameters' folder.
It would also be wise to increase the number of peaks output by decreasing the
threshold fraction of maximum peak height to 0.3 both in
the Rotation Function and Translation Function Parameters folders.
Find 8 peaks above this fraction is probably
enough to get an idea of the influence of noise peaks.
Results of various runs of auto-AMoRe, keeping the sphere volume at 19.396, are summarised in the following table. The resolution range used is 10-3Å. The model is as before.
| model cell | ROTFUN | FITFUN | comments | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| peak nr | CC_F | RF_F | CC_I | CC_P | peak nr | CC_F | RF_F | CC_I | ||
| calculated | 1 | 22.5 | 53.0 | 35.0 | 29.2 | 2 | 83.2 | 26.8 | 83.2 | |
| 2 | 23.4 | 52.8 | 36.3 | 29.2 | 1 | |||||
| 3 | 8.1 | 56.9 | 13.6 | 12.7 | 8 | 24.1 | 55.0 | 24.0 | 4 | 9.8 | 56.5 | 14.5 | 12.2 | 3 | 30.1 | 53.0 | 28.0 |
| 101 101 101 | 1 | 22.6 | 53.0 | 35.1 | 29.4 | 2 | 83.2 | 26.8 | 83.2 | |
| 2 | 23.4 | 52.8 | 36.3 | 29.4 | 1 | |||||
| 3 | 8.0 | 56.9 | 13.5 | 12.5 | 8 | 24.0 | 54.4 | 25.2 | ||
| 4 | 9.8 | 56.6 | 14.5 | 12.2 | 3 | 29.8 | 53.2 | 27.9 | ||
| 91 91 91 | 1 | 22.5 | 53.0 | 35.0 | 29.1 | 2 | 83.2 | 26.8 | 83.2 | |
| 2 | 3 | |||||||||
| 3 | 23.4 | 52.8 | 35.0 | 29.1 | 1 | |||||
| 4 | 8.1 | 56.9 | 13.7 | 12.4 | 7 | 24.1 | 54.9 | 24.0 | ||
| 5 | 9.8 | 56.6 | 14.5 | 12.2 | 4 | 29.8 | 53.2 | 27.9 | ||
| 61 61 61 | 1 | 22.8 | 53.0 | 35.4 | 26.7 | 2 | 83.2 | 26.8 | 83.2 | |
| 2 | 23.7 | 52.7 | 36.7 | 26.7 | 1 | |||||
| 3 | 8.3 | 56.9 | 14.1 | 12.3 | 5 | 24.1 | 54.9 | 24.8 | ||
| 4 | 9.8 | 56.6 | 14.4 | 11.6 | 3 | 29.9 | 53.2 | 27.9 | ||
| 31 31 31 | 1 | 23.0 | 52.8 | 35.3 | 15.1 | 3 | 83.3 | 26.8 | 83.3 | |
| 2 | 24.1 | 52.4 | 37.0 | 14.9 | 1 | 83.2 | 26.8 | 83.2 | ||
| 3 | 23.2 | 52.8 | 36.1 | 14.9 | 2 | |||||
| 4 | 8.4 | 57.2 | 12.9 | 10.6 | 4 | 24.2 | 55.1 | 23.4 | ||
| 21 21 21 | 1 | 18.2 | 54.2 | 28.0 | 11.6 | 4 | 83.3 | 26.8 | 83.2 | |
| 2 | 7.7 | 57.2 | 11.2 | 10.7 | 6 | 23.5 | 55.1 | 21.0 | ||
| 3 | 21.4 | 53.3 | 33.4 | 10.4 | 3 | 83.2 | 26.8 | 83.2 | ||
| 4 | 22.1 | 53.2 | 34.5 | 10.4 | 2 | |||||
| 5 | 1 | |||||||||
| 6 | 9.8 | 56.7 | 14.2 | 9.6 | 5 | 26.2 | 54.0 | 24.8 | ||
| 20 20 20 | 1 | 20.1 | 53.9 | 31.3 | 11.1 | 3 | 83.3 | 26.8 | 83.3 | |
| 2 | 20.2 | 53.7 | 31.5 | 10.9 | 2 | 83.2 | 26.8 | 83.2 | ||
| 3 | 20.7 | 53.6 | 32.3 | 10.9 | 1 | |||||
| 4 | 8.4 | 57.1 | 11.6 | 9.9 | 7 | 23.8 | 55.5 | 22.2 | ||
| 5 | 10.0 | 56.7 | 15.4 | 9.1 | 4 | 29.5 | 52.9 | 27.7 | ||
| 19 19 19 | 1 | 6.2 | 57.7 | 8.1 | 9.4 | 36 | 22.3 | 55.3 | 20.2 | correct solutions not found in the standard search |
| 2 | 7.7 | 57.2 | 10.5 | 8.5 | 11 | 22.8 | 55.5 | 21.9 | ||
| 29 | 14.6 | 55.3 | 22.3 | 7.0 | 1 | 83.3 | 26.8 | 83.3 | ||
| 37 | 13.4 | 55.7 | 21.3 | 6.8 | 2 | |||||
| 18 18 18 | 1 | 9.1 | 57.1 | 14.8 | 10.2 | 2 | 25.9 | 54.6 | 24.7 | only 1 correct solution found, from 100 ROTFUN peaks |
| 2 | 6.3 | 57.7 | 7.8 | 9.0 | 34 | 22.9 | 55.0 | 19.8 | ||
| 27 | 13.9 | 55.6 | 20.9 | 6.9 | 1 | 83.3 | 26.8 | 83.2 | ||
| 11 11 11 | correct solution not found within first 100 ROTFUN peaks | |||||||||
| 91 31 31 | 1 | 24.1 | 52.5 | 37.0 | 25.7 | 1 | 83.2 | 26.8 | 83.2 | |
| 2 | 23.7 | 52.7 | 36.7 | 25.7 | 2 | |||||
| 3 | 8.4 | 57.2 | 12.9 | 11.2 | 4 | 24.9 | 54.8 | 22.4 | ||
| 5 | 9.6 | 56.6 | 14.3 | 10.4 | 3 | 29.9 | 52.6 | 27.4 | ||
| 91 19 19 | 1 | 15.5 | 55.2 | 23.5 | 8.5 | 2 | 83.3 | 26.8 | 83.2 | |
| 2 | 11.9 | 56.0 | 16.9 | 8.5 | 3 | 83.2 | 26.9 | 83.1 | ||
| 3 | 5.6 | 57.7 | 7.3 | 8.5 | 7 | 21.4 | 55.5 | 29.7 | ||
| 5 | 14.2 | 55.7 | 22.8 | 8.2 | 1 | 83.3 | 26.8 | 83.3 | ||
Coming soon.
For more information on the AMoRe program, see AMoRe.
The Interface documentation on features from this tutorial can be found at:
| Molecular Replacement Module |
| File Selection |
| The FileViewer Utility |
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