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[ccp4bb]: Fwd: refmac5 and RNA refinement problem
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Well I found out that this was an artifact due to a non-sequential
numbering scheme in my molecule that unfortunately is established by an
agreed convention. Sorry if I have wasted anyone's time with this.
Bill Scott
Begin forwarded message:
> From: wgscott@chemistry.ucsc.edu
> Date: Fri Jun 28, 2002 12:24:26 PM US/Pacific
> To: "C.C.Ballard" <C.C.Ballard@dl.ac.uk>
> Cc: ccp4bb@dl.ac.uk
> Subject: refmac5 and RNA refinement problem
>
> I am very new to refmac as I was getting frustrated refining an RNA
> molecule in CNS and have found that Refmac5 seemed to be a good
> alternative.
>
> However I am now finding that the bond between the phosphorus atom of
> one nucleotide and the O3' of the next nucleotide appears to have no
> distance restraint that keeps it sensible. Moreover, the worst cases
> always seem to be those in which the O3' is on a U nucleotide.
>
> Any suggestions for how I ought to deal with this? (I've been refining
> along the lines of Example 5 in the CCP4-4.2 documentation for Refmac5.)
>
> Thanks in advance.
>
> Bill Scott
>