Hi Sam
As someone who's built nucleic acids for a long time, I understand the frustration with the RNA nomenclature.
May I suggest using the pdb remediator from the Richardson group (available at http://kinemage.biochem.duke.edu/software/remediator.php) ?
The 'new' (versus using --old) works quite well with coot and RCrane.
F
On Apr 22, 2016, at 2:16 AM, Sam Tang <[log in to unmask]> wrote:
> Hi again
>
> I am wondering if anyone has the experience using a plugin in Coot called RCrane to build RNA and then refine with Refmac. It happens that refmac cannot recognize my di-/tri-nucleotide and complains of missing atoms. No problem for single nucleotides built from the Coot library.
>
> Would be glad if anyone with similar experience could share further on this.
>
> Thanks in advance.
>
> Kind regards
>
> Sam
>
> Biochemistry Programme, School of Life Sciences, CUHK
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