HI Jan, I did use sphere but it does not help since my ligand is still breaking apart. I attached the pdb file of the ligand for you to look at and maybe help me to solve this issue.
Thanks, Anat. -----Original Message----- From: "ing. Jan Stránský" [mailto:[email protected]] Sent: Friday, March 22, 2013 10:44 AM To: Anat Bashan Cc: [email protected] Subject: Re: refining/regularizing a ligand I built 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. > >
ccAaa_200313-coot-0.pdb
Description: ccAaa_200313-coot-0.pdb
