[phenixbb] naive question how to add GTP as a residue to a nucleic acid chain and refine!

Almudena Ponce Salvatierra maps.farma at gmail.com
Fri Apr 12 08:42:45 PDT 2019

Dear all,

I would like to add a GTP residue to a nucleic acid chain. For so I
followed the following steps in coot: add monomer from library, GTP,
changed chain ID and residue number accordingly, and then Extensions -->
Modelling --> link 2 atoms. I got a dashed line between the 3'O of the GTP
and the phosphate of the neighboring nucleotide, and then I used the real
space refine tool. Up to here, it all looked promising.

In phenix refine I run elbow and readyset and provided cif files, but after
phenix.refine I find out that the link between GTP and it's neighbor is

How to preserve the bond?

Thank you very much in advance!!


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