[phenixbb] phenixbb Digest, Vol 80, Issue 1

[Matthew J. Whitley]

Hello,

One simple thing that might be the problem:

As I'm sure you know, oligosaccharides are formed via intermolecular
dehydration reactions.  If I understand you correctly, you built the
oligosaccharide by loading the component monomers into the density in Coot
and then joined them together.  Whenever two sugars are joined together,
three atoms are given off as a water molecule.  Did you actually delete
the appropriate oxygen and two hydrogens from your coordinates for each
glycosidic linkage in your structure?  If you didn't, then it doesn't
matter whether you told Coot or Phenix that the monomers or linked, you'll
still have atoms trying to occupy the same space and thus the refinement
will blow them apart.  Not that I have EVER made that mistake myself . . .

Similar topics have come up on the Phenix BB before.  For other possibly
useful information, see:
http://phenix-online.org/pipermail/phenixbb/2012-April/018390.html
http://www.phenix-online.org/pipermail/phenixbb/2009-October/013951.html

Good luck!
Matthew


---
Matthew J. Whitley, Ph.D.
Postdoctoral Research Fellow
Angela Gronenborn Lab
Department of Structural Biology
University of Pittsburgh School of Medicine

On Wed, July 4, 2012 7:55 pm, phenixbb-request at phenix-online.org wrote:
>
>
> Message: 14
> Date: Wed, 4 Jul 2012 15:28:09 -0400
> From: crystallogrphy <qunwan1 at gmail.com>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: [phenixbb] ask refinement question including an aligo as the
> 	ligand
> Message-ID:
> 	<CANcEHNi95ss+Tst8+8JVTK3=B598HjC_NNg5N7_=6-whdMTXpQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I want to refine my structure including a sugar oligomer as the ligand in
> Phenix GUI.
>
> I first put each subunit into the density and merge them together as the
> oligomer in Coot. Then I merged the oligomer coordinates to the protein
> file. Then I run phenix.elbow to get the cif file. Finally, I run
> phenix.refine. However, the oligomer units were pushed away from each
> other. I guess I need to modify the cif file to link the oligo units
> together. Does anyone know how I can I do it?
>
> thanks!