 |
 |
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, <[log in to unmask]> 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 <[log in to unmask]> wrote: ----- > > To: [log in to unmask] > 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, <[log in to unmask]> 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. >