I fully agree with this!
Best, Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board <[log in to unmask]> Im Auftrag von Phoebe A. Rice
Gesendet: Freitag, 28. Februar 2020 17:03
An: [log in to unmask]
Betreff: [EXTERNAL] Re: [ccp4bb] What resolution - X-ray diffraction round this time
EXTERNAL : Real sender is [log in to unmask]
Can we get some momentum for the "standard table 1" including TWO numbers - outer limit used in refinement, and nominal resolution based on some standard such as I/sigI =2 (or 3, or whatever the community can agree on)? That would hopefully cut down on all the reviewer complaints of overstated resolution.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
Committee on Microbiology
https://urldefense.proofpoint.com/v2/url?u=https-3A__voices.uchicago.edu_phoebericelab_&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=CXNbP2DMixZriXPv1R2bTMMTnMPdy4mwce_8MJuNxlA&e=
On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" <[log in to unmask] on behalf of [log in to unmask]> wrote:
Dear colleagues,
I agree with all the previous responses, it is a pity to throw away
useful high-resolution data. The problem of high-resolution cutoff
estimation is also nicely summarized in another paper by Andrew Karplus
and Kay Diederichs "Assessing and maximizing data quality in
macromolecular crystallography"
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC4684713_&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=lrf35lEnkEOs6pHot-cjxf9f3SI4dmCvkcL4098veOQ&e= . It is suggested
using CC1/2 for the selection of the cutoff for data processing (not
I/sigI or R_whatever). Later on, the decision should be validated
performing the paired refinement protocol.
Good luck with the argumentation.
Martin
On 2/28/20 11:08 AM, LMB wrote:
> Ask the referee - (apart from the other suggestions here)
>
> ‘How would removing data Improve my model?”
>
> Sent from my iPad
>
>> On 28 Feb 2020, at 08:22, dusan turk <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> Browsing through the recent discussion on EM data resolution cutoff
>> it occurred to me that the X-ray diffraction community isn’t that
>> unanimous either.
>>
>> My stand:
>>
>> When the default resolution cutoff provided with the data processing
>> software in electron density map calculation and refinement delivers
>> quality maps noisier than expected and/or too high R-factors I start
>> adjusting the resolution cutoff by lowering the resolution and trying
>> alternative space group. Hence, I allow the data processing programs
>> to suggest where to draw the line (be it CC1/2, I/sigI, R merge, R
>> sym, R p.i.m. and R r.i.m, …) , unless there are problems.
>>
>> Doing so, I came into a dispute with a referee who shaped his request:
>>
>> "It is well accepted that the criteria for resolution cutoff should
>> consider both I/SigI and Rmerge for the outer most shell. For data
>> sets collected at synchrotron sources, the criteria of I/SigI > 5 and
>> Rmerge <50% can be taken as a good practical reference.”
>>
>> So where do we stand? Which are the most objective criteria for
>> resolution cutoff to be used in diffraction data processing? Which
>> number of shells to use when calculating the statistics? Do we have a
>> consensus?
>>
>> best wishes,
>>
>> dusan turk
>>
>>
>>
>> Dr. Dusan Turk, Prof.
>> Head of Structural Biology Group https://urldefense.proofpoint.com/v2/url?u=http-3A__stef.ijs.si_&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=_3e4jARMhVBSasLY6-m9dOnl_vTRnBGwLgzq_9Dv6c8&e=
>> Head of Centre for Protein and Structure Production
>> Centre of excellence for Integrated Approaches in Chemistry and
>> Biology of Proteins, Scientific Director
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cipkebip.org_&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=78xv1Oze-kc7Gv9avvfnElFBluCHaasC65gzTDktaDM&e=
>> e-mail: [log in to unmask]
>> phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biology
>> fax: +386 1 477 3984 Jozef Stefan Institute
>> Jamova 39, 1 000 Ljubljana,Slovenia
>> Skype: dusan.turk (voice over internet: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.skype.com&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=mPvllhErNKtBHfXxbwHETwf1PoZUZaZar8o6ZJCL8TM&e=
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