Dear Mohamed,
adding to what Nicolas says:
zero-dose extrapolation (ZDE) should be able to reduce the influence of _specific_ radiation damage on your data. In a SAD/MAD experiment, this effect may be as large as the anomalous signal itself, _if_ there is radiation damage. So in that case you should try ZDE; I have heard many times from people who could solve the substructure with but not without ZDE.
If the data are for refinement or MR, the small correction won't make a huge difference. In particular, it will not turn data from a damaged crystal into undamaged/good data - if you can visually see (on the frames) that the crystal diffracts worse, then your unspecific damage will most likely dominate the error anyway.
One more thought:it never hurts to try both with and without ZDE. After all, as scientists we learn from doing experiments, not from following rules. Unexpected and interesting findings are only to be discovered when new ways are tried.
good luck,
Kay
On Fri, 2 Oct 2015 14:03:21 +0000, FOOS Nicolas <[log in to unmask]> wrote:
>Dear Mohamed,
My first question is about what do you expect of your data. Depending of your goal, MR or experimental phasing, maybe the strategy will be different.
But according to XDS wiki : "A word of warning: even if the internal quality indicators (R-factors) are better when using this feature, there is no guarantee that the resulting intensities will actually be better suited for your purposes than those obtained without it. In particular, extrapolating to the ends of the dose interval (0 dose and full dose) decreases the precision of the intensities. "
When you collect 360, you increase your multiplicity, but your crystal suffered of radiation damage.
If you are not trying to solve by experimental phasing, maybe it's better to use only one part of you data. Maybe the one which has not too suffered of radiation damage. You can check the INTEGRATE.LP and see from which frame the number of strong spot decrease. It could be an indicator.
In my opinion you have to check you images. See if the last are as good as the first. And if you have a complet dataset without the worst images, it could be good to use only the best parts of the data instead of apply strong correction to compensate the radiation damage and finally lose information which could be averaged.
Maybe i am wrong, some other people can give an advice.
Hope to help
Nicolas
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De : CCP4 bulletin board [[log in to unmask]] de la part de Mohamed Noor [[log in to unmask]]
Envoy� : vendredi 2 octobre 2015 15:31
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Objet : [ccp4bb] XDS/XSCALE - Zero-dose extrapolation
Dear all
I can get a high-multiplicity dataset from the first 180 degrees (SG P41 21 2; about 12 times) and the first 90 degrees (about 6 times). However, I note from CORRECT.LP that based on the asterisk-marked CC(1/2), the difference in the significant/effective highest-resolution shell is 0.3 A (2.2 and 1.9 A, respectively). In this case, is it a good idea to do an extrapolation? If yes, how much data should I be using? The dataset was collected 360 degrees and I have a few more datasets from different crystals as well.
I hope I have included all the relevant information above, if not, I can post more details.
Thanks.
Mohamed
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