Hi Satvik
One thing I don't understand is why there are no dips in your plot for an ice
ring around 3.6Å - for hexagonal ice it should be about as strong as the ring
at 2.25Å. It would be very useful to actually see the images to try to work out
what the real issue is.
I think it would be best to continue this discussion off the ccp4bb and to let
someone with extensive data processing experience have a look at your images.
This will probably be faster and more definitive in the long run.
I will be meeting developers of both XDS and DIALS next week and we should have
some time to spend on your problem if we have access to the original images!
Prof Dodson will also be present so we will be able to make use of her
experience.
The bug concerning the specific resolution range exclusion appears to be quite
long-standing, so I'm not surprised that it is in other versions of iMosflm.
Harry
--
Dr Harry Powell
Chairman of International Union of Crystallography Commission on
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic
Computing)
On 10 Aug 2017, at 11:13, Satvik Kumar wrote:
> Dear Prof. Powell,
>
> In order to get past the bug, I reprocessed the data using a different
> installation of iMOSFLM. The option "automatic ice and powder ring exclusion"
> was toggled ON and also the snowflake button was kept ON during indexing,
> cell refinement and integration. I observe that these changes have improved
> the statics at the cost of completeness. The mean I/sigI has increased from
> -0.2 to 0.4 but the completeness has reduced from 98.2 to 85.5 (64.5 to 31.9,
> outershell).
>
> I inspected the wilson plots carefully but I am unable identify if the
> re-processing has helped (plots are attached).
>
> I am unable to manually exclude specific resolution shells even with this
> different installation of iMOSFLM.
>
> Please share your feedback.
>
> Thanks once again.
>
>
> Best,
> Satvik
>
>
> On Wed, Aug 9, 2017 at 6:15 PM, Harry Powell
> wrote:
> Hi
>> 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
>> 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 wrote:
>> Your plots look strangely different to the old Scala output you posted
>> before, but
