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) <tom.p...@csiro.au> Sent: Sunday, September 12, 2021 5:02:04 AM To: CCP4BB@JISCMAIL.AC.UK; 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 tom.p...@csiro.au ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Petr Kolenko <petr.kole...@fjfi.cvut.cz> Sent: Sunday, September 12, 2021 5:43 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> 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 Upgrade for PHENIX users: 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 Direct link to the video: 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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Tushar R. <rtusha...@gmail.com> Sent: Saturday, September 11, 2021 6:46:32 PM To: CCP4BB@JISCMAIL.AC.UK 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/ Hope this helps. All the best. Best, Tushar. On Sat, 11 Sep 2021, 09:36 Rajiv gandhi.s, <raji....@gmail.com<mailto:raji....@gmail.com>> 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, <taohsin.ch...@gmail.com<mailto:taohsin.ch...@gmail.com>> 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). It may be useful for your case. Best wishes, Tao-Hsin On Sep 11, 2021, at 11:55 AM, Syed Farhan Ali <alifarhan...@gmail.com<mailto:alifarhan...@gmail.com>> 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 <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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: 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 ######################################################################## 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at 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 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/
