Dear Tom, there are a couple of papers (essentially the first one) with a relevant discussion.
Urzhumtseva_2013_ActaCryst_D69_1921-1934 Urzhumtseva_2015_J.Applied Cryst_48_589-597 If you wish I may send you the files (off list). With best regards, Sacha Urzhumtsev ----- Le 13 Sep 21, à 4:42, Peat, Tom (Manufacturing, Clayton) <[email protected]> a écrit : > Thanks to Petr and Ian for their thoughtful replies. > One worry I have is that as a community we continue to debate what is the > 'proper' or 'correct' way to measure resolution which I think is quite > confusing to those that are early in their crystallographic (or general > structural biology) careers. It is the scientific method to argue (sometimes > ad > nauseum) about what constitutes the best data, the best methods, etc. so this > isn't really a surprise to those that have been around a while. But it might > be > nice to have a set of criteria which most people in the field agree to and > then > these are updated on a regular basis as we move forward as a field. Not that > we > will ever get 100% agreement to anything, as that is just unrealistic (and > there are many posts to this BB already to show that). What I was thinking was > a set of standards that are reasonable and that when broken (not all at once, > but one standard at a time), one needs to explain why instead of just hoping > that a reviewer (or other scientist looking at the data) just misses it. From > various posts, it seems that people generally agree that CC1/2 is a good > criteria, that Rpim and Rfree are pretty good criteria, that I/sigI is > reasonable at some level and that completeness and multiplicity (or > redundancy) > are important as well. These are not all independent (Rpim clearly depends on > the multiplicity/redundancy, etc) but having some kind of standard set of > numbers to judge one's own data by as a first pass might be helpful (and I > believe the original question was basically, what do a I report as the > resolution?) > Just to throw some numbers out as an example: CC1/2 at 0.3 (or 30% depending > on > your reporting style), I/sigI at 1.0, completeness at 75% in the last > resolution bin and multiplicity/redundancy at least 3.0 throughout (and in the > last shell). Nothing magical in these numbers, but if you feel that your data > are really good but the completeness isn't there, you just explain why, or > something to that effect. I believe this is one of the reasons we always have > a > table 1 in our publications and that there is no one number that really gives > us that sense of assurance that the model and data are good (or in my own > experience, good enough). > I guess what I am trying to 'solve' is the issue I come across regularly in > reviewing papers: the authors are very interested in the biology of their > system and spend a lot of time explaining what the system is, why it is > important, etc (all great stuff) and then fill in the table with a set of > numbers that makes me then wonder why they believe their own models? Often > very > low completeness, low redundancy/ multiplicity, CC1/2 which varies from 0.99+ > to almost zero, all in order to make the reported resolution sound good (and > crazy numbers of decimal places- reporting a resolution of 1.39623 AA with 15% > completeness could more realistically be reported at 1.40 AA or 1.50 AA with > 50% completeness and I don't think the actual interpretation/ electron density > would change significantly). If it was then stated explicitly in the > manuscript, for example, that paired refinement was done or that difference > maps were calculated (or FEM or Polder or ?) at various resolutions which then > showed the area of interest more clearly, the readers and reviewers might be > more assured that the authors weren't just reporting a semi-random number as > 'the resolution'. Numbers in the table that are clearly (?) a bit relaxed, if > actually explained in the paper, would then make more sense. We as a community > have gone somewhat this direction with the validation criteria given for > deposited structures, which is a start, but it hasn't really tackled the > thorny > question of 'what is my resolution?' > As Ian mentioned, some programs and some criteria depend on relatively high > completeness in the data in the way they are calculated (CC1/2 is perfect when > all data are set to zero). If a program 'fills in' data that are missing, then > that one will also be subject to issues when the data are very incomplete. One > can always call on people to 'get better data' and of course it would always > be > fantastic if each data set was complete, had high CC1/2 and multiplicity/ > redundancy, but then this isn't very realistic either. > Thanks again for the considered replies to the previous post, and if this > sounds > like a rant, it probably is. > cheers, tom > Tom Peat, PhD > Proteins Group > Biomedical Program, CSIRO > 343 Royal Parade > Parkville, VIC, 3052 > +613 9662 7304 > +614 57 539 419 > [email protected] > From: Petr Kolenko <[email protected]> > Sent: Sunday, September 12, 2021 10:07 PM > To: Peat, Tom (Manufacturing, Clayton) <[email protected]>; > [email protected] <[email protected]> > Subject: Re: [ccp4bb] criteria to set resolution limit > Dear Tom, > You are absolutely right with your points. But let me explain a bit more my > opinion. And be aware that it is my opinion! Not necessarily the truth. There > might be another opinion in the community. > In paired refinement, you always have the reference data. In case of > significantly decreasing completeness, you can always select your starting > resolution that is complete enough (e.g. more than 90% ?). And this is your > reference data. As an increase in resolution improves your model (drop in > R-values, mainly R-free), you always compare your models using the reference > data. Should we use as many observables as possible? I would do so. Even if > the > completeness was very low. > Another thing is the statement that your data is processed up to 1.1 AA when > the > completeness is as low as 2%. Of course. But, this is why we have more cells > in > the so-called "Table 1". When judging the structure, one should go carefully > through the whole table. And maybe, more resolution shells should be reported > in extreme cases. There is a possibility to do so during the structure > deposition. Here, I agree with you. > Low data completeness is usually a big problem. Both random and systematic. My > personal experience is that it causes severe instability in structure > refinement. But this is frequently projected to the R-values. And as any > instability appears, paired refinement does not suggest using the higher > resolution. As long as it follows the right trends, you should be fine. > Thanks for pointing out the high data completeness in our paper. We should run > more analyses to get ready for such comments. ;-) > Best regards, > Petr > ________________________________________ > From: Peat, Tom (Manufacturing, Clayton) <[email protected]> > Sent: Sunday, September 12, 2021 5:02:04 AM > To: [email protected]; Petr Kolenko > Subject: Re: [ccp4bb] criteria to set resolution limit > Hello Petr, > I would like to understand more completely your assertion in the last email > regarding completeness: "I would not care about low data completeness in case > when PAIREF shows improvement of your model." > In the papers you gave links to, the data completeness was always 90+% even in > the outer shells. In cases where this is not true, I'm not clear why > completeness would not be important? The ultimate thought experiment, or > extreme case, where one has very few reflections in the resolution limit, just > getting a 'better model' doesn't show me that the structure is now 1.3 A (or > whatever limit one wants to set). Models with no data are perfect, in the > physical sense of not having clashes, Ramachandran outliers, etc. > As an example, I am aware of a deposition in the PDB where the outer > resolution > shell was approximately 2% complete and I don't believe that the structure is > really at the resolution stated as the features 'seen' in terms of electron > density don't really measure up to what I would expect and the electron > density > looks a lot more like about 0.5A lower resolution, where the completeness is a > bit better than 50%. > So my 'bias' is that completeness of the data is still an important feature > that > needs to be taken into account when forming the basis of 'resolution limit', > but I'm absolutely willing to be shown that my bias is incorrect. > Best regards, tom > Tom Peat, PhD > Proteins Group > Biomedical Program, CSIRO > 343 Royal Parade > Parkville, VIC, 3052 > +613 9662 7304 > +614 57 539 419 > [email protected] > ________________________________ > From: CCP4 bulletin board <[email protected]> on behalf of Petr Kolenko > <[email protected]> > Sent: Sunday, September 12, 2021 5:43 AM > To: [email protected] <[email protected]> > Subject: Re: [ccp4bb] criteria to set resolution limit > Dear Farhan, > Your dataset does not seem to be that critically anisotropic to me. But of > course, try the STARANISO server and make your own decision. > To me, the dataset seems to be collected with a suboptimal data strategy. > Although I do not know your setup, I would make the crystal-to-detector > distance shorter next time. Or maybe rotate a bit more with the crystal? I do > not know the details. > And now, to the point of the resolution. The optimal approach is to try paired > refinement, or even better - paired refinement with the complete > cross-validation protocol. This can be done using program PAIREF that is easy > to be installed to your CCP4 installation by the following commands: > ccp4-python -m ensurepip --user > ccp4-python -m pip install pairef --no-deps --upgrade --user > The easiest way to use PAIREF is via GUI. Use the following command: > ccp4-python -m pairef --gui > To know more about the program and about the protocol, please read further. > The original work: [ > https://journals.iucr.org/m/issues/2020/04/00/mf5044/index.html | > https://journals.iucr.org/m/issues/2020/04/00/mf5044/index.html ] > Upgrade for PHENIX users: [ > https://scripts.iucr.org/cgi-bin/paper?S2053230X21006129 | > https://scripts.iucr.org/cgi-bin/paper?S2053230X21006129 ] > We organized a webinar about the PAIREF about a half year ago. We even made a > video from that. The video covers a short introduction to paired refinement, > installation of PAIREF, and running a test case. > The link for the webinar is here: [ > https://pairef.fjfi.cvut.cz/dokuwiki/doku.php?id=webinar_2021-03 | > https://pairef.fjfi.cvut.cz/dokuwiki/doku.php?id=webinar_2021-03 ] > Direct link to the video: [ > https://pairef.fjfi.cvut.cz/docs/pairef_poli_webinar/PAIREF_webinar_23Mar2021_.mp4 > | > https://pairef.fjfi.cvut.cz/docs/pairef_poli_webinar/PAIREF_webinar_23Mar2021_.mp4 > ] > I would not care about low data completeness in case when PAIREF shows > improvement of your model. From my point of view, you have the ideal starting > point. Start with the resolution of 1.8AA and verify, whether the higher > shells > improve your model. I hope you will be able to make the best decision, good > luck! ;-) And do not hesitate to ask me for more details about PAIREF. > Best regards, > Petr > ________________________________________ > From: CCP4 bulletin board <[email protected]> on behalf of Tushar R. > <[email protected]> > Sent: Saturday, September 11, 2021 6:46:32 PM > To: [email protected] > Subject: Re: [ccp4bb] criteria to set resolution limit > Along with the paper mentioned by Rajiv, you could look at this paper as well > which discusses a major shift in the understanding of data quality from > I/sig(I) based to CC1/2 based indicators. > [ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ | > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ ] > Hope this helps. > All the best. > Best, > Tushar. > On Sat, 11 Sep 2021, 09:36 Rajiv gandhi.s, > <[email protected]<mailto:[email protected]>> wrote: > Dear Chang, > One need to set resolution cut off, to have a meaningful data without losing > high resolution data and keeping data integrity. Some key quality indicators > like I/Sigma I, CC 1/2 and Rpim etc., at outer most shell need to be > considered. What was the CC 1/2 value in outer shell ? > Please refer to the below paper. > How good are my data and what is the resolution > Assessing and maximizing data quality in macromolecular crystallograph > On Sat, 11 Sep 2021, 9:52 pm Tao-Hsin Chang, > <[email protected]<mailto:[email protected]>> wrote: > Hi Farhan, > It looks like that your diffraction data has an anisotropic issue and it leads > to the issues of resolution limit, intensity, and completeness. Check The > STARANISO Server ( [ https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi > | https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi ] ). It may be > useful for your case. > Best wishes, > Tao-Hsin > On Sep 11, 2021, at 11:55 AM, Syed Farhan Ali > <[email protected]<mailto:[email protected]>> wrote: > Dear All, > I have query regarding one of my dataset. I am running aimless by keeping > highest resolution 1.62 A and getting I/SigI = 2 but data completeness is > around 22 in outermost shell. And if I am increasing the resolution cutoff up > to 1.8 A then I/SigI is 6.2 and completeness is 82.4. > I have attached the screenshot of the result. > What should be the criteria to set the resolution limit? Should I stick to > I/SigI or I have to consider about the completeness of data. > And if completeness is also a guiding factor than how much minimum > completeness > I can keep in the higher resolution shell. > Regards, > Farhan > ________________________________ > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] > <Screenshot 2021-09-11 at 8.43.25 PM.png><screenshot1.6.tiff> > ________________________________ > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] > ________________________________ > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] > ________________________________ > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] > ######################################################################## > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] > This message was issued to members of [ http://www.jiscmail.ac.uk/CCP4BB | > www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB ] >, a mailing list > hosted by www.jiscmail.ac.uk< [ http://www.jiscmail.ac.uk/ | > http://www.jiscmail.ac.uk ] >, terms & conditions are available at [ > https://www.jiscmail.ac.uk/policyandsecurity/ | > https://www.jiscmail.ac.uk/policyandsecurity/ ] > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
