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Re: [ccp4bb]: Jumping between refinement programs..
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On 14 Aug 00 at 9:50, Eleanor J. Dodson wrote:
> Date: Mon, 14 Aug 2000 09:50:22 +0100
> From: "Eleanor J. Dodson" <firstname.lastname@example.org>
> Reply-to: E.Dodson@ysbl.york.ac.uk
> Organization: Structural Biology Lab. , Dep. Of Chemistry, University of York
> To: email@example.com
> Cc: firstname.lastname@example.org
> Subject: Re: [ccp4bb]: Jumping between refinement programs..
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> 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???
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