Thank you, Bernhard, for poining out this nice paper by Ian, one more that I missed previously.
Best regards, Sacha Urzhumtsev ----- Le 6 Mar 20, à 19:15, Bernhard Rupp <hofkristall...@gmail.com> a écrit : > In addition to Sacha’s work there are a few older papers by Ian Tickle & Cie. > (summarized in BMC) and a figure of the empirical distributions > [ > http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-24.htm > | > http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-24.htm > ] > which are broad and – as mentioned - the actual delta values are context > dependent. > Best, BR > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Andrew Leslie > Sent: Friday, March 6, 2020 08:52 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Overrefinement considerations and Refmac5. > I would like to add a small caveat to Eleanor’s rule about a 3% difference > being > too low for a structure refined against 3Å data. > If the 3Å data is for a structure that has already been solved at much higher > resolution (e.g. 2Å) and the only difference for the 3Å dataset is a different > ligand (say) and the structure is solved by molecular replacement using the > high resolution structure as a model, in those circumstances it is possible > (and quite acceptable) to have a much lower difference between Rwork and Rfree > than one might expect, even at low as 3-4%. > Andrew >> On 6 Mar 2020, at 15:22, Eleanor Dodson < [ >> mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk | >> 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk ] > wrote: >> You dont give the data resolution - that is very important.. >> I hate this rule bound approach to Rfree - R differences.. but as a guide >> No non-crystallographic symmetry. >> 1A data - you would expect them to be almost equal >> 3A data - I would expect a difference of at least 10% - once had the >> pleasure of >> sendng a paper back as unreasonable when the data was only to 3A and the r >> factors differed by 3% >> Pseudo-symmetry and non-crystallographic symmetry can make things more >> complicated. >> Ideally reflections related by such symmetry should match - either set >> belong to >> the Rfree set, or working set. >> The best way to get a low Rfactor and a high Rfree is to have virtually no >> geometric restraints. ie have a very high weighting term. >> The auto selection works pretty well in my experience.. >> Not really an answer but some ideas.. >> Eleanor >> On Fri, 6 Mar 2020 at 13:32, M T < [ mailto:michel...@gmail.com | >> michel...@gmail.com ] > wrote: >>> Dear BBers, >>> I am trying to refine a structure using COOT and Refmac5 and I have some >>> concerns about overrefinement and x-ray term weight in Refmac5, based on the >>> fact that during refinement to let R factor to drift too far from Rfree is >>> not >>> good... >>> So... First question about that : what is too far ? I have some values in >>> mind >>> like 6% of difference is OK, 10% is not... But is there a relation in >>> between >>> resolution of the structure and this difference? Should it be higher at >>> lower >>> resolution, or always around 6-7% independently of the resolution? >>> Second question is, ok, I have a too big difference, lets say 9-10%... What >>> could be the reason of that and on what to play to reduce this difference? >>> One way I choose is to look at the x-ray term weight (even if I am totally >>> sure >>> that Refmac5 is doing things better than me), because I saw that the final >>> rms >>> on BondLength were to constraint (I have in mind that this value should >>> stays >>> in between 0.02 and 0.01). >>> So I looked into Refmac log to know where was the starting point and I found >>> 8.75. >>> Then I tried several tests and here are the results: >>> ************************************************************************* >>> R factor >>> Rfree >>> BondLength >>> BondAngle >>> ChirVolume >>> Auto weighting and experimental sigmas boxes checked >>> 0.1932 >>> 0.2886 >>> 0.0072 >>> 1.6426 >>> 0.1184 >>> Weighting term at 4 and experimental sigmas box checked >>> 0.1780 >>> 0.3159 >>> 0.1047 >>> 8.1929 >>> 0.5937 >>> Weighting term at 4 >>> 0.1792 >>> 0.3143 >>> 0.1008 >>> 7.8200 >>> 0.5667 >>> Weighting term at 15 and experimental sigmas box checked >>> 0.1783 >>> 0.3272 >>> 0.2020 >>> 1.6569 >>> 0.9745 >>> Weighting term at 15 >>> 0.1801 >>> 0.3279 >>> 0.2022 >>> 12.5748 >>> 0.9792 >>> Weighting term at 8.75 >>> 0.1790 >>> 0.3235 >>> 0.1545 >>> 10.5118 >>> 0.7909 >>> Auto weighting box checked >>> 0.1948 >>> 0.2880 >>> 0.0076 >>> 1.6308 >>> 0.1176 >>> Refinement Parameters >>> <image.png> >>> So like nothing looks satisfying I decided to ask my questions here... >>> What do you recommend to fix my problem, which is a too large difference >>> between >>> R and Rfree? >>> Thank you for answers. >>> To unsubscribe from the CCP4BB list, click the following link: >>> [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] >> To unsubscribe from the CCP4BB list, click the following link: >> [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
