Hi Sam,If you haven't, you could watch this video on how to use RCrane:
https://www.youtube.com/watch?v=ZsqAd-BVU50I myself just used it very briefly before and encountered no problem with Refmac. I asked my lab member who built a 20 nt RNA structure with it and encountered no problem with Refmac either.Good luck,ChenOn Tue, Apr 26, 2016 at 8:28 AM, Francis Reyes <[log in to unmask]> wrote: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 https://urldefense.proofpoint.com/v2/url?u=http-3A__kinemage.biochem.duke.edu_software_remediator.php&d=AwIFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=gSXo4C8rqJ9XkrmffW_ue3fdnKcxQ2XBorlZY7APB2A&s=FbYgBE5kA9O2lUoILoZbegODn3aAN9SY0U6C4MuXQ6U&e= ) ?
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