Hi Sarah, I've been experiencing the same issue with building RNA in the latest coot 0.8.9.2-pre builds. I found a workaround by fixing the detached 5' phosphate atom and performing real-space refine on only that nucleotide, then I manually drag the phosphate close enough to the 3' oxygen (~2A) so that coot forms a link after accepting. After that, I unfix the phosphate and perform a real-space on both nucleotides and I find they stay linked.
Hope that helps! Best, Eric ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
