I had processed the images using iMOSFLM. The option of “automatic ice and powder ring exclusion” was toggled ON when I processed the data. It is only now I realize that this is not the way to get rid of ice rings.

This is due to the exclusion limits being set too conservatively for the ice rings; you might consider it a bug, because this should be the way to get rid of the ice rings!

The latest paper on the use of iMOSFLM (Powell. H. R et al, Nature Protocols, 2017) suggests excluding data within specific resolution shells to get rid of the ice ring problem. I observe that if I set the limits 3.62-3.68, 2.23-2.26, 1.90-1.93 Å in “excluded resolution ranges” option of iMOSFLM, only the spots upto 3.6 Å are found and also predicted. Moreover all high resolution data is lost. Somehow I am not able to get this strategy working in iMOSFLM.

This is due to a bug in the iMosflm code; it will be fixed in the next release (I've told the current developer about it...).

I could send you a fix so that this option works if you like.

Harry

Dr Harry Powell

Chairman of International Union of Crystallography Commission on Crystallographic Computing

Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)

On 9 Aug 2017, at 13:17, Satvik Kumar wrote:

Dear All,

Thank you all for your inputs.

You are all correct. The diffraction images have ice rings at 3.67, 2.24 and 1.9 Å. The intensity of these ice rings decrease with increasing resolution. In the Wilson plot, I clearly observe the spikes in intensity corresponding to these resolutions.

The latest paper on the use of iMOSFLM (Powell. H. R et al, Nature Protocols, 2017) suggests excluding data within specific resolution shells to get rid of the ice ring problem. I observe that if I set the limits 3.62-3.68, 2.23-2.26, 1.90-1.93 Å in “excluded resolution ranges” option of iMOSFLM, only the spots upto 3.6 Å are found and also predicted. Moreover all high resolution data is lost. Somehow I am not able to get this strategy working in iMOSFLM.

The other suggestion was to deice using AUSPEX or DEICE. The information available on the internet suggests AUSPEX is a diagnostic tool. Is it possible to use it to deice? I will be trying to get DEICE working shortly.

Please share your thoughts as to how I should proceed.

Thanks,
Satvik

On Tue, Aug 8, 2017 at 11:47 PM, Eleanor Dodson <[log in to unmask]> wrote:
You have some horrible ice rings - some data processing software may be able to cut them out.. how are you processing it?
Eleanor

On 8 August 2017 at 15:43, Christian Roth <[log in to unmask]> wrote:

Your plots look strangely different to the old Scala output you posted before, but never mind.
Paul is right that a negative intensity is not desired and your crystal has some issues with ice.

That one icering around 2.26 must be massive taken into account how haywire your curve goes there.

Have you had a look at the images? There should be something visible in that area.

Christian

Am 08.08.2017 um 15:17 schrieb Paul Emsley:

On 08/08/2017 15:07, Satvik Kumar wrote:

Dear Prof. Powell and Prof. Dodson,

Thanks for your reply and advise.

As per your suggestion, I have re-scaled the intensities using Aimless at 1.861 A.

I observe that the I/sigI has dropped to -0.8

That's not good.

> and the behaviour of CC_1/2 is still anomalous.

That made me laugh out loud. Perhaps not the best choice of adjective.

Also, when I inspect the Wilson plot (Fig. 1), I observe that the curve does not fall smoothly with respect to the reference curve (blue). Even with respect to one more Wilson plot from CCP4 website (Fig. 2), the curve from my aimless output is different and discontinuous.

Icy!

/me wonders if CCP4 are distributing auspex yet...

The second moment of I is constant only up to a resolution of 2.4 Å at a value of 3 (Fig. 3). I was not able to get some other plot to compare against mine.

Please tell me if I can still go ahead and refine at 1.861 A.

No you can't.

Maybe with some chopping you can rescue some reflections beyond 2.1.

Paul

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