Hi Anat,
have you tried Sphere refine?
Jan
On 03/20/2013 02:24 PM, Anat Bashan wrote:
Hi All,
I build a ligand that is partly RNA and Partly a protein chain. In between I
have a special nucleotide with a N bound to C3' (instead of O3'). it is :
CC-PPU-Ala-Phe-Val. I have links in the .pdb file and the PPU is a known ligand
to COOT. My links connect the N3' of the PPU with the C of Ala. nevertheless,
if I try to regularize or refine the Ala keeps moving away from the PPU. The
other link I defined between the C and the PPU works fine.
What am I missing here ?
Do I need to specify anything else than the LINK?
I attached the .pdb file of my ligand for you to be able to load into coot and
try playing with it yourself.
I look forward for your help.
Best, Anat.
