Re: [ccp4bb] Ice ring data issue

[Andrew Leslie]

Apologies if this is a duplicate, not clear if the Email I sent 5 hours ago 
actually got sent.


Hi Alex,

 Although there is an “ice” icon in the imosflm GUI, which excludes 
all resolution bins where ice ringss are possible, this is not the best way to 
deal with this. Instead, use the Settings -> Processing options -> Processing 
tab, where you can specify individual resolution ranges to be excluded from the 
integration.

The important thing here is to make sure that the resolution range you specify 
is generous enough. Looking at an image and holding down the Ctrl key to give 
you the resolution where the mouse pointer is positioned, you need to make sure 
that you specify resolution limits that are a bit below (on the low resolution 
side) and above (on the high resolution side) the ice ring itself. This is 
because if any part of the measurement box extends into the ice ring it can 
affect the integration, and the measurement box is larger than the actual spot 
size.

This will, of course, affect your overall completeness, but it should get rid 
of the reflections with anomalous intensity. I find that the easiest way to 
check this is to look at the Wilson plot produced by ctruncate (one of the post 
you get when you run QuickScale).

Best wishes,

Andrew



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Re: [ccp4bb] Ice ring data issue

[Andrew Leslie]

Hi Alex,

 Although there is an “ice” icon in the imosflm GUI, which excludes 
all resolution bins where ice ringss are possible, this is not the best way to 
deal with this. Instead, use the Settings -> Processing options -> Processing 
tab, where you can specify individual resolution ranges to be excluded from the 
integration.

The important thing here is to make sure that the resolution range you specify 
is generous enough. Looking at an image and holding down the Ctrl key to give 
you the resolution where the mouse pointer is positioned, you need to make sure 
that you specify resolution limits that are a bit below (on the low resolution 
side) and above (on the high resolution side) the ice ring itself. This is 
because if any part of the measurement box extends into the ice ring it can 
affect the integration, and the measurement box is larger than the actual spot 
size.

This will, of course, affect your overall completeness, but it should get rid 
of the reflections with anomalous intensity. I find that the easiest way to 
check this is to look at the Wilson plot produced by ctruncate (one of the post 
you get when you run QuickScale).

Best wishes,

Andrew



> On 4 Mar 2021, at 15:39, Alexander Brown  
> wrote:
> 
> Hi all,
> I'm struggling with a dataset I have which shows very poor data quality 
> around 3.6A, or exactly where I can see a significant ice ring in the images. 
> I'm trying to use mosflm to process the image files, and I have seen a 
> previous thread on the message board where it is recommended to turn on three 
> tick boxes for ice ring exclusion, but despite this, as I continue through 
> the processing sequence and use aimless, it still flags that the data is 
> affected by an ice ring at that resolution, which you can also see in the 
> quality/resolution graphs. 
> 
> I have even tried making a mask in the moslfm viewer using the mask tool to 
> cover the entire ice ring, but to no avail.
> 
> Finally I did have a go at using EVAL which is mentioned in the original post 
> about ice rings, but it seems it depends on libgfortran3 packages which have 
> now been replaced with libgfortran5 and so I didn't get very far.
> 
> Is there a manual way to mask out certain data, or could there be something 
> with my data that is causing the automatic ice ring resolution not to be as 
> effective?
> 
> Thank you!
> 
> Alex Brown
> 
> PhD Student
> School of Pharmacy
> Biodiscovery Institute (previously Centre for Biomolecular sciences)
> University of Nottingham
> Nottingham
> NG7 2RD 
> 
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> 
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> communications with the University of Nottingham may be monitored 
> where permitted by law.
> 
> 
> 
> 
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Re: [ccp4bb] Ice ring data issue

[Paul Emsley]

It might just be possible that background modelling of diffraction data 
in the presence of ice rings is better done in more modern software.


Paul.


On 06/03/2021 00:10, Edward A. Berry wrote:
(Obviously this is for culling the bad data after data reduction is 
complete- doesn't do anything to prevent the ice ring from introducing 
error in the scaling process. Not really what you were asking for, and 
maybe not even useful now, given automatic outlier rejection in 
today's programs)


On 03/05/2021 04:00 PM, Edward A. Berry wrote:
For manually masking out the rings, you can use mtz2various to dump 
reflections in resolution ranges without ice in ascii, cat them all 
together and use f2mtz to read them into a new mtz file. Example 
attached.


You might also be able to do it using mtzutils to write out mtz files 
in limited resolution ranges, and then to merge them back into one file.


On 03/04/2021 10:39 AM, Alexander Brown wrote:

Hi all,
I'm struggling with a dataset I have which shows very poor data 
quality around 3.6A, or exactly where I can see a significant ice 
ring in the images. I'm trying to use mosflm to process the image 
files, and I have seen a previous thread on the message board where 
it is recommended to turn on three tick boxes for ice ring 
exclusion, but despite this, as I continue through the processing 
sequence and use aimless, it still flags that the data is affected 
by an ice ring at that resolution, which you can also see in the 
quality/resolution graphs.


I have even tried making a mask in the moslfm viewer using the mask 
tool to cover the entire ice ring, but to no avail.


Finally I did have a go at using EVAL which is mentioned in the 
original post about ice rings, but it seems it depends on 
libgfortran3 packages which have now been replaced with libgfortran5 
and so I didn't get very far.


Is there a manual way to mask out certain data, or could there be 
something with my data that is causing the automatic ice ring 
resolution not to be as effective?






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Re: [ccp4bb] Ice ring data issue

[Edward A. Berry]

(Obviously this is for culling the bad data after data reduction is complete- 
doesn't do anything to prevent the ice ring from introducing error in the 
scaling process. Not really what you were asking for, and maybe not even useful 
now, given automatic outlier rejection in today's programs)

On 03/05/2021 04:00 PM, Edward A. Berry wrote:

For manually masking out the rings, you can use mtz2various to dump reflections 
in resolution ranges without ice in ascii, cat them all together and use f2mtz 
to read them into a new mtz file. Example attached.

You might also be able to do it using mtzutils to write out mtz files in 
limited resolution ranges, and then to merge them back into one file.

On 03/04/2021 10:39 AM, Alexander Brown wrote:

Hi all,
I'm struggling with a dataset I have which shows very poor data quality around 
3.6A, or exactly where I can see a significant ice ring in the images. I'm 
trying to use mosflm to process the image files, and I have seen a previous 
thread on the message board where it is recommended to turn on three tick boxes 
for ice ring exclusion, but despite this, as I continue through the processing 
sequence and use aimless, it still flags that the data is affected by an ice 
ring at that resolution, which you can also see in the quality/resolution 
graphs.

I have even tried making a mask in the moslfm viewer using the mask tool to 
cover the entire ice ring, but to no avail.

Finally I did have a go at using EVAL which is mentioned in the original post 
about ice rings, but it seems it depends on libgfortran3 packages which have 
now been replaced with libgfortran5 and so I didn't get very far.

Is there a manual way to mask out certain data, or could there be something 
with my data that is causing the automatic ice ring resolution not to be as 
effective?

Thank you!

*Alex Brown*


PhD Student

School of Pharmacy

Biodiscovery Institute (previously Centre for Biomolecular sciences)

University of Nottingham

Nottingham

NG7 2RD


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Re: [ccp4bb] [EXTERNAL] [ccp4bb] Ice ring data issue

[Edward A. Berry]

For manually masking out the rings, you can use mtz2various to dump reflections 
in resolution ranges without ice in ascii, cat them all together and use f2mtz 
to read them into a new mtz file. Example attached.

You might also be able to do it using mtzutils to write out mtz files in 
limited resolution ranges, and then to merge them back into one file.

On 03/04/2021 10:39 AM, Alexander Brown wrote:

Hi all,
I'm struggling with a dataset I have which shows very poor data quality around 
3.6A, or exactly where I can see a significant ice ring in the images. I'm 
trying to use mosflm to process the image files, and I have seen a previous 
thread on the message board where it is recommended to turn on three tick boxes 
for ice ring exclusion, but despite this, as I continue through the processing 
sequence and use aimless, it still flags that the data is affected by an ice 
ring at that resolution, which you can also see in the quality/resolution 
graphs.

I have even tried making a mask in the moslfm viewer using the mask tool to 
cover the entire ice ring, but to no avail.

Finally I did have a go at using EVAL which is mentioned in the original post 
about ice rings, but it seems it depends on libgfortran3 packages which have 
now been replaced with libgfortran5 and so I didn't get very far.

Is there a manual way to mask out certain data, or could there be something 
with my data that is causing the automatic ice ring resolution not to be as 
effective?

Thank you!

*Alex Brown*


PhD Student

School of Pharmacy

Biodiscovery Institute (previously Centre for Biomolecular sciences)

University of Nottingham

Nottingham

NG7 2RD


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and may contain confidential information. If you have received this
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icefilter.csh
Description: C-Shell script

Re: [ccp4bb] Ice ring data issue

[Harry Powell - CCP4BB]

Hi Alex

Have a look at Auspex - it may be able to help

AUSPEX (www.auspex.de)

Harry

> On 4 Mar 2021, at 15:39, Alexander Brown  
> wrote:
> 
> Hi all,
> I'm struggling with a dataset I have which shows very poor data quality 
> around 3.6A, or exactly where I can see a significant ice ring in the images. 
> I'm trying to use mosflm to process the image files, and I have seen a 
> previous thread on the message board where it is recommended to turn on three 
> tick boxes for ice ring exclusion, but despite this, as I continue through 
> the processing sequence and use aimless, it still flags that the data is 
> affected by an ice ring at that resolution, which you can also see in the 
> quality/resolution graphs. 
> 
> I have even tried making a mask in the moslfm viewer using the mask tool to 
> cover the entire ice ring, but to no avail.
> 
> Finally I did have a go at using EVAL which is mentioned in the original post 
> about ice rings, but it seems it depends on libgfortran3 packages which have 
> now been replaced with libgfortran5 and so I didn't get very far.
> 
> Is there a manual way to mask out certain data, or could there be something 
> with my data that is causing the automatic ice ring resolution not to be as 
> effective?
> 
> Thank you!
> 
> Alex Brown
> 
> PhD Student
> School of Pharmacy
> Biodiscovery Institute (previously Centre for Biomolecular sciences)
> University of Nottingham
> Nottingham
> NG7 2RD 
> This message and any attachment are intended solely for the addressee
> and may contain confidential information. If you have received this
> message in error, please contact the sender and delete the email and
> attachment. 
> 
> Any views or opinions expressed by the author of this email do not
> necessarily reflect the views of the University of Nottingham. Email
> communications with the University of Nottingham may be monitored 
> where permitted by law.
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Ice ring data issue

[Alexander Brown]

Hi all,
I'm struggling with a dataset I have which shows very poor data quality around 
3.6A, or exactly where I can see a significant ice ring in the images. I'm 
trying to use mosflm to process the image files, and I have seen a previous 
thread on the message board where it is recommended to turn on three tick boxes 
for ice ring exclusion, but despite this, as I continue through the processing 
sequence and use aimless, it still flags that the data is affected by an ice 
ring at that resolution, which you can also see in the quality/resolution 
graphs.

I have even tried making a mask in the moslfm viewer using the mask tool to 
cover the entire ice ring, but to no avail.

Finally I did have a go at using EVAL which is mentioned in the original post 
about ice rings, but it seems it depends on libgfortran3 packages which have 
now been replaced with libgfortran5 and so I didn't get very far.

Is there a manual way to mask out certain data, or could there be something 
with my data that is causing the automatic ice ring resolution not to be as 
effective?

Thank you!


Alex Brown


PhD Student

School of Pharmacy

Biodiscovery Institute (previously Centre for Biomolecular sciences)

University of Nottingham

Nottingham

NG7 2RD



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and may contain confidential information. If you have received this
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