[phenixbb] Refining sucrose

ChenTiantian chentiantian2010 at gmail.com
Wed May 25 00:09:47 PDT 2011

I found that the cif file of ligand from ProDRG server is not good for
I always got my ligand pdb file using ProDRG, and use the refmac file as the
restraint file of the ligand, but I found that after running the
phenix.refine, the rmsANGLE is very high.
the I followed someone's advice, using phenix.elbow to produce the ligand's
cif file, that really make sense, now I can easily get the refinement value
of the complex structure in a
reasonable level.
Hope it works with your structure too.


On Tue, May 24, 2011 at 3:34 PM, Priit Eek <priit.eek at gmail.com> wrote:

> Thanks Nigel and Yuri! elbow.where_is_that_cif_file gave me the right cif
> to use in coot. Off to fix that sucrose now...
> Priit
> On 23.05.2011, at 17:55, Yuri wrote:
> > All coot needs to run its real-space refinement is a .cif file as Nigel
> pointed out.
> > You can also get this file from other ligand library websites (proDrg,
> hic-cup, etc...). The only catch here is. The name of your sucrose atoms
> must match, exactly, those in the file.
> > Once you have such file go to the the file drop-down menu and click on
> Import CIF dictionary in coot. That should enable to rotate the rotatable
> bonds of your ligand
> >
> > --
> > Yuri Pompeu
> > _______________________________________________
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