It is always hard to know when to stop tweaking a model.. We know from high resolution studies that many sidechains at the solvent interface have multiple conformations, and that as a result the water networks should also have partial occupancies. But usually correcting these details does not change the Rfactors at all - nor contribute much to the biological relevance of your structure! So often the point to stop is when you get fed up, Phil Evans said years ago - I spend 95% of my time on 5% of the structure, most of which is unimportant.. In practice I let the difference maps decide when to stop - 10 Sigma peak - think why - lots of 5 Sigma positive and negative ones not so important Eleanor
On Tue, 20 Oct 2020 at 11:27, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > A practice that was very popular before the Rfree came around was to fit a > water molecule in every noise peak. One would get spectacular low Rfactors > this way, but I cannot imagine that anyone would believe that this would be > fitting and not over-fitting. > > > > Best, > > Herman > > > > *Von:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *Im Auftrag von *Sam > Tang > *Gesendet:* Dienstag, 20. Oktober 2020 05:27 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [ccp4bb] over-fitting? over-refinement? > > > > Hi, the question may be a bit weird, but how do you define 'over-fitting' > in the context of structure refinement? From users' perspective the > practical aspect is to 'fit' the model into the density. So there comes > this question from our juniors: fit is fit, how is a model over-fit? > > > > BRS > > > > Sam > > > ------------------------------ > > 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7Cfca18f01417745b3655008d874a81d74%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C637387612965782189%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=s1FpY1ufI7De3N6J2%2FivUy4zehp%2BcGl1gGjHeNrzUeA%3D&reserved=0> > > ------------------------------ > > 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/
