How & where are your data collected?

Eleanor

On 9 August 2017 at 13:17, Satvik Kumar <kumarsatvi...@gmail.com> 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.
>
>
> 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.
>
>
> 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 <eleanor.dod...@york.ac.uk
> > 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 <christianroth...@gmail.com>
>> 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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