[phenixbb] refinement with a covalent inhibitor.

Maia Cherney chern at ualberta.ca
Thu Mar 19 10:28:13 PDT 2009

Hi Nigel,
Thank you for your help. The sugar chain is the same, but the crystal 
form is different and the sugar chain is not infinite, because a part of 
the chain is disordered. (To make the complex, I used a high molecular 
weight sugar, 17 or 30 KDa).  Did you get the E64 carboxyl group flat?
I have no trouble with covalent linking, just the geometry of the 
ligands. Do you need my pdb?


Nigel W Moriarty wrote:
> Maia
> I took a look at the PDB entry 3C9E.  The covalently bound ligand can be 
> taken care of using the CIF link files.  The chain of sugars is a 
> different matter.  There is a LINK to a symmetry copy such that the 
> chain continues into the next ASU forming an infinite chain.  I've 
> started working on code to generate the needed files for refinement.  If 
> you need the files today, I can generated them with my test code and you 
> can use them with the current version of PHENIX.
> Is the sugar chain the same as in 3C9E?
> Nigel

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