[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

R-free and map calculations

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Hi All,

	Can anyone enlighten me on the following two 

1: Rfree:-
	It was mentioned in the literature that R-free,
a global indicator of the correctness of the model, is 
calculated using a TEST set of reflections (between a 
minimum of ~500 reflections to a maximum of ~2,000 
reflections). Literature (Kleywegt & Jones (1997) 
Methods in Enzymology, vol.277, 208-230) also suggests that 
for a better model, it is WISE to include the TEST set of 
reflections for map calculations.

	My question is, 

	Incorporation of all reflections while calculating
a 2Fo-Fc/Fo-Fc or sigmaA style 2mFo-DFc/mFo-DFc maps won't
bias Rfree ?

	So in case of a less complete data-set (say around 65% 
overall completeness), one cannot then afford to omit those 
TEST set of reflections for refinement/map calculation?

2: Simulated Annealing:-

	Reports say that Simulated Annealing in Torsion angle 
space (Torsion angle MD refinement?) decreases the number of 
degrees of freedom (to N/3) as compared to that of Cartesian 
coordinate space (=3N; where N=no. of atoms). Also, it was 
mentioned that this method proves to have a LARGE value of 
radius of convergence..

	Can anyone please explain this in brief?

Bye and Regards,
| S.Ravichandran                              e-mail:-                |
| Crystallography &                           ravi@cmb2.saha.ernet.in |
| Molecular Biology Division,                 ravichu@hotmail.com     |
| Saha Institute of Nuclear Physics                                   |
| I/AF, Bidhan Nagar, Calcutta 700 064.       FAX:-                   |
| Calcutta - 700 064. INDIA.                  (91)(033)-337-4637      |
|                                                                     |
|		URL:	http://cmb2.saha.ernet.in/ravi.html           |
"Creativity is great, but plagiarism is faster" - The Law of Motivation