Dear Mohamed,
You can control how xia2 determines the resolution cutoff, e.g. these are the parameters we are currently running xia2 with at Diamond:
-misigma 1 -isigma 0.25 -cc_half 0.5
Here -misigma is the cutoff for the merged <I/sigI> and -isigma the cutoff for the unmerged <I/sigI>.
Regarding your second point, if you are concerned at all about this, you could easily test your hypothesis by re-running xia2 providing the resolution estimated in the previous step via the parameter d_min= and comparing the results between the two data processing runs.
As to comparing XDS and DIALS, the answer is probably similar to that you would get if you were to ask to compare XDS with MOSFLM or HKL2000: "it depends". Most data processing software probably give similar results for the vast majority of datasets, and it is likely only for a few difficult cases where any given program may outperform the other. It is probably mostly personal preference and ease of use that determines which software package most people use, and I imagine that most people are happy to try all available software in difficult cases. Whilst we haven't performed a systematic comparison with other software, we as DIALS developers have had positive reports from users regarding data quality, although equally we are also aware of some datasets where DIALS processing could be improved. DIALS is rapidly developing software, and we are constantly striving to improve it (as, I imagine, are all software developers). One of the advantages of using xia2 is that you can easily perform the comparison yourself for any given dataset by processing your data with DIALS, MOSFLM and XDS.
Having multiple options for performing any one task is undoubtedly a benefit to the wider community, as it increases the likelihood that at least one will work for any given dataset, as well as the added benefit of healthy competition between developers of different software hopefully resulting in constant improvements to software.
Cheers,
Richard
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Mohamed Noor [[log in to unmask]]
Sent: 08 November 2015 17:34
To: ccp4bb
Subject: [ccp4bb] Xia2 resolution cut-off
Dear all
According to the Xia2 blog (http://xia2.blogspot.ie/2010/12/resolution-limits-in-xia2.html and http://xia2.blogspot.ie/2014/03/incoming-feature-resolution-limits-from.html) and a rather old thread ([log in to unmask])" target="_blank">https:[log in to unmask]), there is an automatic resolution cut-off applied. I have a few questions about this:
1. What is the cut-off when CC1/2 is used? Any way of overriding it?
2. Is there a 'danger' of including noise* during the integration step such that it affects scaling later on?
3. For those regular users of Xia2, is there any difference between XDS and DIALS? I know this can be a bit controversial, so off-line replies would be fine - I can summarize it later.
* The crystals diffract to different resolution - some 6 A, some 4 and the best one is 3.4 when processed in a quick-and-dirty way with XDS. The data will be used for molecular replacement.
Thanks.
Mohamed
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