Hello again.
I agree the get-around strategy we took is not a good practice at all.
For our initial imosflm run we actually turned on 'exclude ice ring'
button. The following was reported in the log:
ICE RING SUMMARY:
reso ice_ring mean_I mean_Sigma Estimated_I Ratio Zscore Completeness
Ave_Completeness
3.88 yes 39933.04 3690.30 1398.21 28.56 10.44 0.48
nan
3.67 yes 44809.76 4257.56 778.04 57.59 10.34 0.58
nan
3.43 yes 7270.25 885.61 532.75 13.65 7.61 0.54
nan
2.66 yes 2070.19 488.66 156.09 13.26 3.92 0.46
nan
A total of >2200 reflections were already omited.
The range of poor R seems to correlate to the range 3.8-3.6A. I am thus
also thinking there may be other issues (not visibly identified on images)
other than ice rings.
We actually first merged the two datasets (high and low resolutions) in
pointless before presenting to aimless.
We are trying over other different strategies to see if we can get a better
tackle. Will report again soon.
Sam
On Tue, 9 Apr 2019 at 18:47, Johan Turkenburg <
00002a539df422fe-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> I agree with Harry that an ice ring should never require you to process
> the data in two separate runs, and hopefully this does not become a
> standard approach..........
>
> How did you present those data to aimless so it could scale the two
> datasets that have no overlap at all?
>
> Johan
>
> On Tue, 9 Apr 2019 at 10:07, Harry Powell <
> 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hi Sam
>>
>> Did you use the ice-ring exclusion option in iMosflm (a button that has
>> an image like a snowflake)? It should exclude data in _narrow_ resolution
>> rings (substantially less than 0.2Å!) around the ice rings, and can be set
>> for any combination of indexing, refinement and integration. There should
>> not be any need to process the data twice, once for the low resolution data
>> and once for the high.
>>
>> Harry
>> --
>> Dr Harry Powell
>>
>>
>> ------------------------------
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>> On 8 Apr 2019, at 19:50, Sam Tang wrote:
>>
>> Hello everyone
>>
>> Thanks a lot for your input and advices. To report on how we tackled the
>> issue -
>>
>> (1) We used imosflm to integrate the data.
>> (2) We eventually integrated the data in two resolution ranges, say
>> 45A-3.5A, and 3.3A-3A, and merge them by Aimless. I must add that indeed
>> from the log file for our initial round the program had already identified
>> some ice ring regions.
>>
>> Aimless statistics looked fine and we were able to get a MR solution
>> which was refined to much better Rf/Rw.
>>
>> This is definitely not a smart solution because we effectively 'throw
>> away' useful data between 3.5A-3.3A, but for the purpose of MR and
>> refinement, it seems we have solved (or simply bypassed?) the problem.
>>
>> Suggestions on XDS/DIALS are appreciated. We are actually using this
>> dataset as a test set for XDS/DIALS to deal with ice rings. Will further
>> report if we've got anything interesting.
>>
>> Thanks again!
>>
>> Sam
>>
>>
>>
>>
>> On Thu, 4 Apr 2019 at 20:54, Clemens Vonrhein <vonrh...@globalphasing.com>
>> wrote:
>>
>>> Dear all,
>>>
>>> And if you want to process with XDS: autoPROC [1] will try to detect
>>> and exclude ice-rings automatically - if present [2].
>>>
>>> If you know that you have ice-rings you can force it [3] to exclude
>>> all known ice-rings ranges - but this might not be the best solution
>>> if you have "just" diffuse ice-rings (where the special treatment of
>>> background within DIALS might be better). Something to test and
>>> compare maybe?
>>>
>>> Cheers
>>>
>>> Clemens
>>>
>>> [1] https://www.globalphasing.com/autoproc/
>>>
>>> https://www.globalphasing.com/autoproc/wiki/index.cgi?IceRingHandling
>>> [2]
>>> https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_spotnohkl
>>>
>>> https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings
>>> [3]
>>> https://www.globalphasing.com/autoproc/manual/appendix1.html#SetvarParameter_XdsExcludeIceRingsAutomatically
>>>
>>> On Thu, Apr 04, 2019 at 10:51:19AM +0000, melanie.voll...@diamond.ac.uk
>>> wrote:
>>> > Dear Sam,
>>> >
>>> >
>>> > to continue from James Parkhurst's email...
>>> >
>>> >
>>> > You can do more analysis regarding ice rings using Auspex (
>>> https://www.auspex.de/) if you already have some integrated file.
>>> >
>>> > Regarding re-integrating images, what did you use the first time
>>> round? I think if you use DIALS it got some clever implementation in it
>>> that is better in estimating the errors of reflections in proximity to ice
>>> rings. Hence you should get better Rfactors without having to remove the
>>> effected resolution range and the data it covers (
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/).
>>> >
>>> >
>>> > HTH
>>> >
>>> >
>>> > M
>>> >
>>> >
>>> > ________________________________
>>> > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
>>> herman.schreu...@sanofi.com <herman.schreu...@sanofi.com>
>>> > Sent: 04 April 2019 10:26:09
>>> > To: ccp4bb
>>> > Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>>> >
>>> >
>>> > Dear Sam,
>>> >
>>> >
>>> >
>>> > I would remove the ice ring and reprocess the data. Ice rings may
>>> wreak havoc with scaling so at minimum you have to redo the scaling.
>>> >
>>> >
>>> >
>>> > Best,
>>> >
>>> > Herman
>>> >
>>> >
>>> >
>>> > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
>>> von Sam Tang
>>> > Gesendet: Donnerstag, 4. April 2019 11:01
>>> > An: CCP4BB@JISCMAIL.AC.UK
>>> > Betreff: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>>> >
>>> >
>>> >
>>> >
>>> > Dear Eleanor and Eric
>>> >
>>> >
>>> >
>>> > Thanks for your replies.
>>> >
>>> >
>>> >
>>> > Yes indeed when we looked at the plots e.g. R factor vs resln there
>>> was a sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring
>>> on the image. Thus our first thought was to remove the ic ring. (either
>>> reprocess or can we bypass this resolution range during refinement?)
>>> >
>>> >
>>> >
>>> > The protein is 50 kDa, two molecule in the ASU, seemingly no obvious
>>> density was unassigned. We got ~30000 total observations, ~15000 unique
>>> observations. NCS restraints was applied.
>>> >
>>> >
>>> >
>>> > Best regards
>>> >
>>> > Sam
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > On Thu, 4 Apr 2019 at 08:57, Eric Montemayor <
>>> montemayor.e...@gmail.com<mailto:montemayor.e...@gmail.com>> wrote:
>>> >
>>> > That’s a rather large gap between Rwork and Rfree. I suspect you have
>>> mis-assigned your space group and as a result have a large number of copies
>>> in your asymmetric unit. Any structure can be solved in P1, but that does
>>> not mean the true space group is indeed P1. If you use P1 when it’s not
>>> actually P1, you will have an unnecessarily overparamerized model, hence
>>> the large gap between Rwork and Rfree.
>>> >
>>> >
>>> >
>>> > Questions:
>>> >
>>> > 1- how many copies in your asymmetric unit in P1?
>>> >
>>> > 2- how many atoms in your model vs number of unique reflections?
>>> >
>>> > 3- if more than one copy per asymmetric unit, are you imposing NCS
>>> restraints during refinement?
>>> >
>>> >
>>> >
>>> > -Eric
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > On Wed, Apr 3, 2019 at 1:41 PM Sam Tang <samtys0...@gmail.com<mailto:
>>> samtys0...@gmail.com>> wrote:
>>> >
>>> > Hi everyone again
>>> >
>>> >
>>> >
>>> > Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
>>> after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
>>> structure was solved by MR and current model seems to fit density well. In
>>> Refmac log I found that at the resolution corresponding to high R there may
>>> be a solvent/ice ring. Since imosflm should be able to exclude ice rings, I
>>> am not 100% sure whether it's the cause to high R. But if this is actually
>>> the case, is there a way I can exclude certain resolution bins during
>>> Refmac (and is it an appropriate way to do so?)
>>> >
>>> >
>>> >
>>> > PS - the data is not affected by twining or pseudosymmetry as checked
>>> by Xtriage.
>>> >
>>> >
>>> >
>>> > Many thanks!
>>> >
>>> >
>>> >
>>> > Sam
>>> >
>>> >
>>> >
>>> > ________________________________
>>> >
>>> > To unsubscribe from the CCP4BB list, click the following link:
>>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=UECB-BTblxRTCrEA2arfPs5VNLr4ntyGxszsw_5Jaxc&s=QloAn3zc13ZQX64uxy6UZygomHXUigCIkpTw8ZhYpbk&e=
>>> >
>>> >
>>> >
>>> >
>>> > ________________________________
>>> >
>>> > To unsubscribe from the CCP4BB list, click the following link:
>>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=UECB-BTblxRTCrEA2arfPs5VNLr4ntyGxszsw_5Jaxc&s=QloAn3zc13ZQX64uxy6UZygomHXUigCIkpTw8ZhYpbk&e=
>>> >
>>> >
>>> > ________________________________
>>> >
>>> > To unsubscribe from the CCP4BB list, click the following link:
>>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>> >
>>> > --
>>> > This e-mail and any attachments may contain confidential, copyright
>>> and or privileged material, and are for the use of the intended addressee
>>> only. If you are not the intended addressee or an authorised recipient of
>>> the addressee please notify us of receipt by returning the e-mail and do
>>> not use, copy, retain, distribute or disclose the information in or
>>> attached to the e-mail.
>>> > Any opinions expressed within this e-mail are those of the individual
>>> and not necessarily of Diamond Light Source Ltd.
>>> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
>>> attachments are free from viruses and we cannot accept liability for any
>>> damage which you may sustain as a result of software viruses which may be
>>> transmitted in or with the message.
>>> > Diamond Light Source Limited (company no. 4375679). Registered in
>>> England and Wales with its registered office at Diamond House, Harwell
>>> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>>> >
>>> >
>>> >
>>> ########################################################################
>>> >
>>> > To unsubscribe from the CCP4BB list, click the following link:
>>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>>
>>> --
>>>
>>> *--------------------------------------------------------------
>>> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
>>> * Global Phasing Ltd., Sheraton House, Castle Park
>>> * Cambridge CB3 0AX, UK www.globalphasing.com
>>> *--------------------------------------------------------------
>>>
>>> ########################################################################
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>>
>>
>> ------------------------------
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>>
>>
>> ------------------------------
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>
>
> --
> Dr. Johan P. Turkenburg X-ray facilities manager
> York Structural Biology Laboratory
> University of York
> York YO10 5DD UK Phone (+) 44 1904 328251
> http://orcid.org/0000-0001-6992-6838
> EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
> <http://orcid.org/0000-0001-6992-6838>
>
> ------------------------------
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
