Thanks for your replies. I did use default settings in phenix refine, included TLS in it. This is an about 2.3A data, and the number Rfree used to refine is big enough. I also kept the same Rfree in two programs. In refmac I also tried diffenrent weighting sets--from defaut 0.3 to 0.02, TLS included--maybe there are some other ways to define the restrains. The R and Rfree will increase as the weighting is set too low, and the gap didnot improve much. I donnot know in this case if the phenix refine has converged, but the not stable Rfree in refmac made me nervous. Simply, in this case, which one should I choose? Certainly to my private opinion I would prefer to Scott's answer, Rfree is the most obvious parameter than something esle like geometry, eg. Just looks good. :)
On 3/5/08, Partha Chakrabarti <[EMAIL PROTECTED]> wrote: > > One point which I don't understand is how can someone compare the two > different programs when they don't use the same numbers for > xray:geometry terms? Taking the default settings for a given > resolution might not be enough.. ! > > > > > On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides > <[EMAIL PROTECTED]> wrote: > > Hi Yang > > how many reflections do you have in your test-set for calculating > > R-free? Too few reflections, typically less than 500, may not > > constitute a statistically robust cross-validation data set, and thus > may > > lead to fluctuations in R-free plus a tendency for R-free to increase > > as a function of refinement cycle. Some of the early > > publications from Axel Brunger on crystallographic cross-validation > > address the need for enough reflections (>500) in the test-set. In > > addition, the presence of even a handful of strong but inaccurately > > measured/integrated low-resolution reflections in a limited test-set > > can aggravate abnormal behavior in R-free. > > > > Best wishes > > Savvas > > > > > > toQuoting yang li <[EMAIL PROTECTED]>: > > > > > Dear All, > > > I have post a similar question about CNS and refmac before, now > in > > > another structure I met a similar problem. I have an almost finished > > > structure, the Rfree of which > > > is about 0.28 by refmac. Then I used phenix to refine it, below is > the > > > result: > > > REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS > > > ******************* > > > REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = > 1.213 > > > REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = > 1.374 > > > REMARK > > > > ************************************************************************ > > > Since the map from phenix couldnot be opened by coot directly--or > I > > > donnot know how to--I used refmac to get a mtz map file. But I found > that at > > > the first several cycle of > > > refmac the Rfree decreased, then both the R and Rfree > values continued > > > increasing and FOM decreasing. > > > The best R/Rfree/FOM during the refinement is > > > > > > > ----------------------------------------------------------------------------- > > > Overall R factor = 0.1932 > > > Free R factor = 0.2513 > > > Overall figure of merit = 0.8168 > > > > ----------------------------------------------------------------------------- > > > And after 40 cycles the final result is: > > > > ----------------------------------------------------------------------------- > > > Overall R factor = 0.2008 > > > Free R factor = 0.2772 > > > Overall figure of merit = 0.7902 > > > > ----------------------------------------------------------------------------- > > > The values looks like keep going up if increase the cycles. Then > which > > > value should I take as the final result? The phenix or the best > Refmac > > > result or I have to take a converged > > > value from refmac? > > > > > > > > > > -- > MRC National Institute for Medical Research > Division of Molecular Structure > The Ridgeway, NW7 1AA, UK > Email: [EMAIL PROTECTED] > Phone: + 44 208 816 2515 >
