Hi, I am very thankful to all who responded to my queries. But I am still not very clear about the concept of detwinning the data if refinement of twinned data using *_twin.inp (CNS inputs) works well. What could be the reason to put detwin_*.inp file in the CNS directory xtal_twin which is meant for refining twinned data. Also in CCP4 package, there is a program called "detwin" and then refine normally.
Thanking you all again. --- Yours Sincerely, Shankar Prasad Kanaujia Bioinformatics Center, Department of SERC IISc, Bangalore - 12, INDIA. Mobile: 9845631581 On Thu, 1 Feb 2007, Debanu Das wrote: > Hi Shankar, > I believe it is better to use CNS make_cv_twin.inp to define the > reflections related by the twin operator and then use this cv file to carry > out refinement using the twin_lsq refinement target in CNS than to actually > try to detwin the data and then carry out refinement with the detwinned data. > I had a similar case recently (also at 2.0A) and also found better R/Rfree > values on using the first approach. > > However, I think it is also possible that one of the above approaches may work > better than the other (in terms of R/Rfree and resulting map quality after > refinement) depending on the twin fraction, kind of twinning, etc. so it is > better to try both as you have done. I think whichever method gives better > maps and R/Rfree value should be used. > > However, I'm not sure why there is such a difference in R-factor values in the > 2 approaches, mainly because I don't understand the details of twinning very > well. > > Regards, > Debanu. > > Shankar Prasad Kanaujia wrote: > > > Dear all, > > I am refining a twinned (twinning fraction = 0.213 from Yeates' method) data > > using CNS. I refined in two ways. > > 1. Firstly, I created the .cv file using make_cv_twin.inp from CNS and then > > e.g. used minimize_twin.inp for minimization. The Rwork and Rfree were > > 19.55% and 22.06% respectively. > > 2. In the second case, I detwinned the .cv file (.cv file created in the > > first case) using detwin_partial.inp from CNS. And then e.g. used > > minimize.inp for minimization (Here, I am refining as there is no twinning). > > The Rwork and Rfree were 24.5% and 26.59% respectively. > > > > In both cases, I used the same model and without any water. The resolution > > of the data is 2.0 Angs, space group R3, twinning operator (h,-h-k,-l) > > > > By seeing the Rwork and Rfree, I can guess that first case is better. I also > > superimposed two minimized pdb's and RMSD = 0.123 Angs. > > > > Now My question is which of the above two ways is the right way to refine > > the model. And why there is almost 5% difference in R-factor values. > > > > Any suggestions or references will be highly appreciated. Thanking you all > > in advance. > > > > -- > > Yours Sincerely, > > Shankar Prasad Kanaujia > > IISc, Bangalore - 12 > > Mobile: 9845631581 > >
