Dear all, I am sorry for a late reply. R-values should not exceed 0.42 which happened in your case for shells 1.91-1.83 and 1.83-1.77. It is because theoretically (under some assumptions), a perfect model gives an R value of 0.42 against random data (Evans & Murshudov 2013 https://doi.org/10.1107/S0907444913000061 ). So as David wrote, your data are not better than 1.9 A. I would refine the structure against data at resolution of 2.2 A (including modelling of water molecules), then run paired refinement to add resolution shells 2.2- 2.1, 2.1-2.0 and 2.0-1.9A and choose an optimal high-resolution cutoff according results. Feel free to ask.
"the actual reflections used in calculations and reported statistics may be different (in phenix.refine)" Thank for this comment, this was new for me, good to know! I can imagine it can cause misleading situations/interpretations... Nowadays, I quite often hear an opinion "You do not have to cut your data at high-resolution, refinement program will put low weights for noisy high-resolution reflections so they will not harm your model." I just would like to ask Pavel and other refinement experts - would you dis/agree? Such an approach should be possible by principle but R- values etc. look quite ugly then. Best wishes, Martin On Wed, 2024-01-17 at 18:15 -0800, Pavel Afonine wrote: > Hi Liliana, > > a few things to consider: > > 0) There is a Phenix mailing list for Phenix specific questions > (phenixbb); > > 1) Bin completeness depends on (obviously) how binning is done > (number of reflections per bin or number of bins or binning in d^2 or > d^3 spacing or log-binning etc etc etc) -- all of this will affect > the number of reflections in the "highest resolution bin" and > corresponding statistics. And..."how binning is done" wildly differs > by the program used or even within the same program! > > 2) Refinement (in Phenix) as well as many other Phenix tools apply > temporary reflection omission according to the Read (1999) paper > (Acta Cryst. (1999). D55, 1759-1764). This means while you have so > many reflections in your input reflection file, the actual > reflections used in calculations and reported statistics may be > different. Most logs files keep a good record of this, meaning you > can track this down by inspecting logs files carefully. > > Let me know if you need more assistance with this issue. > > Cheers, > Pavel > > On Wed, Jan 17, 2024 at 1:43 PM David Briggs > <david.bri...@crick.ac.uk> wrote: > > Hi Liliana, > > Two things leap out at me when I look at your data summary. > > > > (1) Your data probably do not go to 1.77Å. The CC1/2 in your outer > > shell is below any of the usual thresholds. There are discussions > > to be had about what the threshold is, but normally CC1/2 values of > > 0.5 or sometimes 0.3 are used. You should also consider I/sigI. > > > > (2) I believe that by default Phenix.refine excludes weaker > > reflections from refinement, which leads to the discrepancy in > > completeness statistics. As your data do not extend as far as what > > is contained in your mtz file, Phenix excludes those essentially > > "empty" reflections. Judging by the Phenix refine output, I would > > estimate your data goes to somewhere around 1.9Å > > > > The program Pairef can help inform your choice of high-resolution > > cutoff. > > > > This can be run from CCP4cloud, but is also available for Phenix, I > > believe. > > > > See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248825/ > > > > Hope this helps, > > > > Dave > > > > > > Dr David C. Briggs CSci MRSB > > Principal Laboratory Research Scientist > > Signalling and Structural Biology Lab > > The Francis Crick Institute > > London, UK > > == > > about.me/david_briggs > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of > > Liliana Margent <lmarg...@gradcenter.cuny.edu> > > Sent: Wednesday, January 17, 2024 9:19:36 PM > > To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > > Subject: [ccp4bb] Resolution Discrepancy in Data Set > > > > External Sender: Use caution. > > > > > > Hello all, > > > > I hope this message finds you well. > > > > In my current data set, I’ve encountered a discrepancy between the > > completeness in the high-resolution shells in merged statistics vs > > the refinement statistics. For example, when I look at my merged > > statistics file, output by Xia2 dials, the completeness in the > > high-resolution shells are 97.6%. When I take this data and > > subsequently refine it in PHENIX I get extremely different > > completeness ranges in the high-resolution shells, but I cannot > > figure out why this large difference is occurring. I’m reaching out > > to you, our esteemed community, for any insights or advice you > > might have. Has anyone else faced a similar challenge? If so, how > > did you navigate through it? Your experiences and suggestions > > could be invaluable in helping me understand and resolve this > > issue. > > > > Thank you in advance for your time and expertise. > > > > Best regards, > > Liliana > > > > see a side-by-side image of the files I mention in the message in > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1Y783MzlnqVwXRCtiLeV0Y2EpmkeDL2nd%2Fview%3Fusp%3Dsharing&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5XcApcqvUkuvjz9oGUsaFpvnfY2p2X1LDE8G4XhFkuo%3D&reserved=0 > > > > ################################################################### > > ##### > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gS2JOO3L%2BYCu2GmMo6I9ajQZn9ZiyZTLzYEZ7CfJN2Q%3D&reserved=0 > > > > This message was issued to members of > > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=y27c8QI3JX%2BYozm2TcSLZlj%2Fo2rOxLUhAJAdwxpxzp8%3D&reserved=0 > > , a mailing list hosted by > > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=sJz0AxBNJb5PxOlNT9%2FKN9MobG2EKXURC67CNB4qbnE%3D&reserved=0 > > , terms & conditions are available at > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7C%7Cb15f2dcfd7804db15e8808dc17a23ef1%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638411232808490947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KIkPxpkW00RhNR7ODU%2F1EFLtP6HAd5Jg2r2K5bUC9Tc%3D&reserved=0 > > The Francis Crick Institute Limited is a registered charity in > > England and Wales no. 1140062 and a company registered in England > > and Wales no. 06885462, with its registered office at 1 Midland > > Road London NW1 1AT > > > > > > 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, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
