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

Re: [ccp4bb]: Jumping between refinement programs..



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

On 14 Aug 00 at 9:50, Eleanor J. Dodson wrote:

> Date:          Mon, 14 Aug 2000 09:50:22 +0100
> From:          "Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>
> Reply-to:      E.Dodson@ysbl.york.ac.uk
> Organization:  Structural Biology Lab. , Dep. Of Chemistry, University of York
> To:            tommi.kajander@helsinki.fi
> Cc:            ccp4bb@dl.ac.uk
> Subject:       Re: [ccp4bb]: Jumping between refinement programs..

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

>  Are you preserving the same FreeR set in both procedures ? but if not
> you are 
> a) not using maximum likelihood properly, since the basis of it is that
> there isa cross validation set to estimate the overall "error- ie D". 
> and b) allowing Refmac/Arp/Warp to use your FreeR set for refinement,
> which will obv. reduce the R factor for that set of data, then going
> back into refinement alone, and excluding them. 
> 
>  The best way is to make sure that the mtz file and the CNS file share
> the same Free R set - if you use f2mtz to make the mtz file with an
> appropriate label for the test set; FreeR_flag is the standard, then the
> uniqueify script it will sort this out .. 
> uniquify -f FreeR_flag CNS.mtz 
>  Eleanor Dodson


 --I was using the same r-free set in _CNS_, but not in ARP, since 
thought it woudln't really matter there since i am only using it to 
add some waters --  it woudl have been best to convert the CNS file 
to mtz with Rree-flag and all. But i am not sure i understand why 
there would be this effect of lowered R-free, as i am using the same 
R-free-set in CNS beofre and after going to ARP???

regards,
Tommi 
Tommi Kajander
Institute for biotechnology
Structural biology/cultivator building
P.O. Box 56
00014 University of Helsinki
tel:+358-9-19158956
fax:+358-9-19158952