Hi your X-ray weight of .08 seems very small, the optimal value is normally in the range 1 to 4 (I usually set it initially at the median, i.e. 2.5). But which weight keyword did you use "WEIGHT MATRIX .08" or "WEIGHT AUTO .08" (the latter is I think undocumented, so I'm guessing the first)? Anyway I would strongly advise the latter: the difference is that the MATRIX weight is on a completely arbitrary scale, whereas the AUTO weight is at least relative to the theoretical value of 1 (even though the optimal value may not be 1 in practice, at least your initial guess will be in the same ball park). Note that what Refmac calls "automatic weighting" is not the same as what X-PLOR, CNS & phenix call "automatic weighting" (at least that's my understanding). "WEIGHT AUTO" in Refmac is the same as "WEIGHT AUTO 10", whereas auto-weighting in X-PLOR corresponds to "WEIGHT AUTO 1" in Refmac. Not surprisingly these give quite different results!
The optimal B factor weight is also around 1, see the paper for typical values. I'm still not clear precisely what you meant by ""there was quite a difference". I don't see that big a difference between the 2 runs, just a slight tightening up of the geometry. Are you saying you see big differences in the refined co-ordinates? That would be a cause for concern. Cheers -- Ian On Fri, Oct 14, 2011 at 11:19 AM, <ka...@rishi.serc.iisc.ernet.in> wrote: > Respected Sir, > > For one of the structures that I did optimisation > had values - (resolution of the data - 2.35Ang) > > Before optimization- (Bfactor weight=1.0, X-ray Weight - auto) > R factor 0.2362 > R free 0.2924 > -LLfree 7521.8 > rmsBOND 0.0160 > zBOND 0.660 > > After optimisation- (B-factor weight=0.2, X-ray Weight - 0.08) > R factor 0.2327 > R free 0.2882 > -LLfree 7495.7 > rmsBOND 0.0111 > zBOND 0.460 > > Also can you tell me what is the limit for B-factor weight hat can be varied. > > Thanking you > With Regards > M. Kavyashree > > > 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 >> > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > >
