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:[log in to unmask]]
Sent: Friday, March 22, 2013 10:44 AM
To: Anat Bashan
Cc: [log in to unmask]
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.
>
>
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