Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

Harry Powell Tue, 09 Apr 2019 02:08:04 -0700

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

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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
>
>
>
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* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park
* Cambridge CB3 0AX, UK www.globalphasing.com
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

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