Sorry I just re-read your last email and realised and didn't read it properly the first time. But what I said still stands: you can of course try to optimise the weights at an early stage (before adding waters say), there's no harm doing that, but there's also not much point since you'll have to do it all again with the complete model, since adding a lot of waters will undoubtedly change the optimal weights. So I just leave the weight optimisation until the model is complete. As long as the initial weights are "in the same ball park", so that your RMSZ(bonds) is around 0.5 for typical resolutions (a bit lower for low resolution, a bit higher for very high resolution) it won't affect interpretation of maps etc.
Cheers -- Ian On Fri, Oct 14, 2011 at 9:37 AM, Ian Tickle <ianj...@gmail.com> wrote: > It must be the same complete model that you refined previously, I > doubt that it will give the correct answer if you leave out the waters > for example. > > You say "there was quite a difference". Could you be more specific: > what were the values of the weights, R factors and RMSZ(bonds/angles) > before and after weight optimisation? > > Cheers > > -- Ian > > On Fri, Oct 14, 2011 at 8:42 AM, <ka...@ssl.serc.iisc.ernet.in> wrote: >> Respected Sir, >> >> Thank you for your clarification. I had adopted this >> method recently. My doubt was if we have to optimize >> these two parameters during refinement, should we have >> the whole model along with water and ligands or only >> protein with few water positioning is enough. The reason >> why I am asking because there was quite a difference >> when I refined the same structure without the optimization >> and with optimization of these two parameters. >> >> Thanking you >> With regards >> M. Kavyashree >> >> -----CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> wrote: ----- >> >> To: CCP4BB@JISCMAIL.AC.UK >> From: Ian Tickle >> Sent by: CCP4 bulletin board >> Date: 10/14/2011 12:34PM >> Subject: Re: [ccp4bb] Optimisation of weights >> >> Hi Kavya >> >> The resolutions of the structures mentioned in the paper were only >> examples, the Rfree/-LLfree minimisation method (which are actually >> due to Axel Brunger & Gerard Bricogne respectively) does not depend on >> resolution. >> >> If the structures are already solved & refined, you don't need to do >> any model building, it should be within the radius of convergence with >> the new weights - it's only a small adjustment after all. >> >> Cheers >> >> -- Ian >> >> On Fri, Oct 14, 2011 at 6:12 AM, <ka...@ssl.serc.iisc.ernet.in> wrote: >> > Dear users, >> > >> > Can the optimization of the X-ray weighing factor >> > and B-factor (overall wt) as mentioned in the paper >> > Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel, >> > be used for the refinement of the data sets beyond >> > the resolution range mentioned in the paper: 1.33 - >> > 2.55 Ang? >> > >> > Also the structures that were used to optimize these >> > parameters were already solved and refined, so when >> > we are solving a new structure to what extent does the >> > model has to be built before starting the optimization? >> > >> > Thanking you >> > With Regards >> > M. Kavyashree >> > >> > >> > -- >> > This message has been scanned for viruses and >> > dangerous content by MailScanner, and is >> > believed to be clean. >> > >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >
