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
Dear Shankar,
the detwinning procedure increases the errors of the observed F's. This
is particularly dramatic for twinning fractions close to 0.5. This
probably explains the higher Rvalues using detwinned data.
Twinned data have a tendancy to look quite good concerning the Rmerge,
as the proportion of weak reflections is smaller.
For similar reasons the refinement against twinned data appear to yield
relatively low R-factors.
I think in the end both of your refinements will give about the same
result and the real R-factor would be in the middle of the two values
obtained by the different techniques.
Greetings
Wim Burmeister
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Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9 FRANCE
E-mail: [EMAIL PROTECTED]
Tel: +33 (0) 476 20 72 82 Fax: +33 (0) 476 20 94 00
http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro
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