Re: [ccp4bb] doubt regarding setting resolution cutoff

[Harry Powell]

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:
>> 

Re: [ccp4bb] doubt regarding setting resolution cutoff

[Harry Powell]

Hi again

I've just been looking through the Mosflm source code - in your case the limits 
you have set (if they worked, but because of a bug they don't) would exclude 
considerably more data than the default values in Mosflm, so I would be 
inclined to use the "exclude ice rings during integration" button in iMosflm 
rather than follow our advice in the Nature Protocols paper.

Sorry if this is a little confusing.

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 13:45, 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 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 

Re: [ccp4bb] doubt regarding setting resolution cutoff

[Harry Powell]

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 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 
>> 
> 
> 
> 
> <090817.pdf>

Re: [ccp4bb] doubt regarding setting resolution cutoff

[Eleanor Dodson]

How & where are your data collected?

Eleanor

On 9 August 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.
>
>
> 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  > 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 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
>>>
>>>
>>>
>>
>

Re: [ccp4bb] doubt regarding setting resolution cutoff

[Eleanor Dodson]

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 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
>
>
>

Re: [ccp4bb] doubt regarding setting resolution cutoff

[Christian Roth]

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

Re: [ccp4bb] doubt regarding setting resolution cutoff

[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

Re: [ccp4bb] doubt regarding setting resolution cutoff

[Eleanor Dodson]

First comment - your data looks excelent - even to 1.8A.

Second - look also at the wilson plot and second moment plots - these
should not be jerky - wilson plot falling off smoothly, 2nd moment pretty
constant to the good resolution limit..

Thirdly - just use all your data and check the refinement results. You can
always reject some later if the refinement looks bizarre.

Eleanor





On 4 August 2017 at 15:37, Harry Powell  wrote:

> Hi Satvik
>
> If you're only just starting out, the first thing I would recommend is
> that you forget all about Scala! It's been effectively obsolete for 5-6
> years, and any bugs that exist in it will not be fixed.
>
> It was replaced by Aimless a long time ago; Aimless is much faster than
> Scala and the scaling model is somewhat improved (what would you expect
> with another half-decade of development?).
>
> Cutting your data at the data processing stage is probably too early in
> the structure solution process.
>
> In your case, I'd continue analysing your structure with all your data (to
> 1.861Å,) after re-scaling with Aimless ;-), then once the structure is
> complete and refined, use the "paired refinement" technique to see if the
> high resolution data are actually contributing any useful information.
>
> HTH
>
> Harry
> --
> Dr Harry Powell
> Chairman of International Union of Crystallography Commission on
> Crystallographic Computing
> Chairman of European Crystallographic Association SIG9 (Crystallographic
> Computing)
>
>
>
> On 4 Aug 2017, at 13:48, Satvik Kumar wrote:
>
> Dear Crystallographers,
>
>
> I am a beginner to solving structures by x-ray crystallography. Having
> collected a diffraction data set using laboratory source X-ray, I am now
> processing the data. I have integrated the data successfully with the
> program iMOSFLM using the space group P212121.
>
>
> During the process of scaling and merging intensities using Scala, I was
> confronted with the question of setting the resolution cutoff. To clear the
> doubts I had, I have read the below articles with great care:
>
>
> 1. How good are my data and what is the resolution? Evans and Murshdov,
> 2013.
>
> 2. Assessing and maximizing data quality in macromolecular
> crystallography. Karplus and Diederichs, 2015.
>
>
> Based on these articles it becomes very clear that I should set the
> resolution cutoff to a value at which CC1/2 reduces to 0.2-0.4 irrespective
> of the values of either Rmerge or I/sigI (prone to uncertainities).
>
>
> When I ran the program Scala using high resolution cutoffs ranging from
> 1.861 A (resolution at which data was collected) to 2.33 A, I observe that
> at 2.0 A, the CC1/2 is 0.582 (outer shell) but the CC1/2 increases to 0.722
> at 1.861 A.
>
>
> The Karplus and Diederichs article clearly states that the CC1/2 is 1 at
> low resolution and drops down with increasing resolution. It also states
> that any anomaly should be carefully inspected.
>
>
> I request the community to kindly inspect the statistics and guide me in
> setting the optimum resolution cutoff. I have attached a pdf file
> containing the Scala outputs (statistics and a plot of correlation
> coefficients versus resolution) for your inspection.
>
>
>
> Thanks,
>
> Satvik
> <040817_scala.pdf>
>
>
>

Re: [ccp4bb] doubt regarding setting resolution cutoff

[Harry Powell]

Hi Satvik

If you're only just starting out, the first thing I would recommend is that you 
forget all about Scala! It's been effectively obsolete for 5-6 years, and any 
bugs that exist in it will not be fixed. 

It was replaced by Aimless a long time ago; Aimless is much faster than Scala 
and the scaling model is somewhat improved (what would you expect with another 
half-decade of development?).

Cutting your data at the data processing stage is probably too early in the 
structure solution process.

In your case, I'd continue analysing your structure with all your data (to 
1.861Å,) after re-scaling with Aimless ;-), then once the structure is complete 
and refined, use the "paired refinement" technique to see if the high 
resolution data are actually contributing any useful information.

HTH

Harry
--
Dr Harry Powell
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 



On 4 Aug 2017, at 13:48, Satvik Kumar wrote:

> Dear Crystallographers,
> 
> 
> 
> I am a beginner to solving structures by x-ray crystallography. Having 
> collected a diffraction data set using laboratory source X-ray, I am now 
> processing the data. I have integrated the data successfully with the program 
> iMOSFLM using the space group P212121. 
> 
> 
> 
> During the process of scaling and merging intensities using Scala, I was 
> confronted with the question of setting the resolution cutoff. To clear the 
> doubts I had, I have read the below articles with great care:
> 
> 
> 
> 1. How good are my data and what is the resolution? Evans and Murshdov, 2013.
> 
> 2. Assessing and maximizing data quality in macromolecular crystallography. 
> Karplus and Diederichs, 2015.
> 
> 
> 
> Based on these articles it becomes very clear that I should set the 
> resolution cutoff to a value at which CC1/2 reduces to 0.2-0.4 irrespective 
> of the values of either Rmerge or I/sigI (prone to uncertainities).
> 
> 
> 
> When I ran the program Scala using high resolution cutoffs ranging from 1.861 
> A (resolution at which data was collected) to 2.33 A, I observe that at 2.0 
> A, the CC1/2 is 0.582 (outer shell) but the CC1/2 increases to 0.722 at 1.861 
> A.
> 
> 
> 
> The Karplus and Diederichs article clearly states that the CC1/2 is 1 at low 
> resolution and drops down with increasing resolution. It also states that any 
> anomaly should be carefully inspected.
> 
> 
> 
> I request the community to kindly inspect the statistics and guide me in 
> setting the optimum resolution cutoff. I have attached a pdf file containing 
> the Scala outputs (statistics and a plot of correlation coefficients versus 
> resolution) for your inspection.
> 
> 
> 
> 
> 
> Thanks,
> 
> Satvik
> 
> <040817_scala.pdf>