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
>
>
