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Xds maxcc12: Difference between revisions
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To analyze XDS_ASCII.HKL in terms of the detailed course of CC<sub>1/2</sub> by frame number and resolution, you could use the program [ | To analyze XDS_ASCII.HKL in terms of the detailed course of CC<sub>1/2</sub> by frame number and resolution, you could use the program [https://{{SERVERNAME}}/pub/xds_maxcc12.linux64 XDS_MAXCC12] , to be stored as xds_maxcc12 in your ~/bin or (as root) in /usr/local/bin (don't forget to chmod a+x xds_maxcc12 !). | ||
You also need a script such as | You also need a script such as | ||
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set out 'xds_maxcc12.ps' | set out 'xds_maxcc12.ps' | ||
set yrange [0:100] | set yrange [0:100] | ||
set xlabel "frame" | |||
set ylabel "%" | |||
set multiplot layout 3,1 | set multiplot layout 3,1 | ||
set title "CC1/2_iso" | set title "CC1/2_iso" | ||
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which you save as plot_maxcc12.rc in your ~/bin or (as root) in /usr/local/bin . | which you save as plot_maxcc12.rc in your ~/bin or (as root) in /usr/local/bin . | ||
Now, after processing a dataset with XDS, you can simply use plot_maxcc12.rc and get | Now, after processing a dataset with XDS, you can simply use plot_maxcc12.rc and get a plot like | ||
[[File:xds_maxcc12.png]] | [[File:xds_maxcc12.png]] | ||
The plot is useful because it shows you the cumulative influence of frames of the dataset on CC<sub>1/2</sub> and completeness of ten resolution shells (to change that number, you must modify the script). The highest resolution shell us usually the lowest curve (red); the curves above are lower resolution shells. (To see the legend which maps the colors and linetypes to resolution range numbers, remove the "set nokey" line in the script) | |||
This may shed light on the usefulness of certain frame ranges of your dataset which have high R<sub>meas</sub>. Do they really compromise CC<sub>1/2</sub> of the merged data - which is all you should care about? | |||
The example plot shows that CC<sub>1/2</sub> is highest around frame 60 to 70 and then gets lower due to radiation damage. However it also makes clear that around frame 60, the completeness is only about 50%. In this case, the anomalous signal is practically just noise. | |||
Clearly, to reliably calculate CC<sub>1/2</sub> requires some multiplicity which is normally not available if the completeness is low. So expect a very noisy CC<sub>1/2</sub> plot at low completeness. At reasonable completeness, however, the plots are quite stable and you can nicely see what e.g radiation does: it hurts the high resolution shells and lets their CC<sub>1/2</sub> degrade. | |||
So the program may serve the purpose of helping to define the cutoff point beyond which frames are discarded due to radiation damage. I find that this cutoff point can be found satisfactorily with the help of this program. Of course the frame cutoff depends on the high resolution cutoff ! The procedure I suggest is: pick the highest resolution cutoff that has still significant signal (marked with "*" in CORRECT.LP), and define the frame cutoff as the frame where the CC<sub>1/2</sub> curve of this resolution range does no longer rise (i.e. becomes constant). | |||
Alternatively, you may base your decision on the anomalous CC<sub>1/2</sub> (bottom plot); the outcome may of course be different then. | |||