Dear all,
I'd like to come back to the question of how useful it is to exclude certain ranges of frames from processing.
I wrote a program xds_maxcc12 which lets you answer this question for your XDS_ASCII.HKL file. Essentially, it calculates the cumulative CC1/2 (isomorphous and anomalous) in (e.g. ten) resolution ranges as a function of the number of frames included in the calculation. So, when you suspect that a given frame range is harmful to your overall data quality (as measured by CC1/2 - but that is reasonable because a low CC1/2 limits the model quality!) then you can simply check whether those frames make CC1/2 drop substantially.
Clearly, to reliably calculate CC1/2 requires some multiplicity which is normally not available if the completeness is low. So expect a very noisy CC1/2 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 CC1/2 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 CC1/2 curve of this resolution range does no longer rise (i.e. becomes constant).
Alternatively, you may base your decision on the anomalous CC1/2; the outcome may of course be different then.
A link to a Linux 64bit binary and some description with script and example plot are in XDSwiki, in the article "Xds_maxcc12". If the program crashes pls tell me about it.
I hope this is useful! The plots are a bit crowded and could probably be presented better, but the information is there ...
Kay
P.S. Before anybody asks: there is currently no "feature" in XDS that lets you choose a high resolution cutoff based on a frame number.
On Thu, 21 Jan 2016 00:47:20 +0000, Mohamed Noor <[log in to unmask]> wrote:
>Dear all
>
>I have a 180-degree dataset (1800 frames) collected at peak wavelength for Fe (for an MR-SAD structure solution). While analyzing the XDS_ASCII.HKL file with Aimless, I noticed something went wrong with a few frames around 1400-1600 (the Rmerge vs. batch plot is attached). When I processed only the first 1200 frames, Aimless indicated a significant anomalous signal up to 3.5 A whereas with the whole dataset (1800 frames), it was only about 7 A. I am trying to process the first 1200 or so images and the last 200 with XDS. How can I achieve this when XDS accepts only one DATA_RANGE line?
>
>As this was the only crystal diffracted, I am trying to squeeze as much as I can out of what I have. The point group is either P 6 or P 6 2 2, not entirely sure yet.
>
>Thanks.
>Mohamed
>
|