Dear Maike,
As you might we have been developing macromolecular refinements methods based on linear scaling QM approaches (Borbulevych et al. Acta Cryst., 2014, D70, 1233-1247; Acta Cryst., 2016, D72, 586-598). One benefit of the QM refinement in PHENIX is that it objectively reveal the ligand geometry and does not rely on provided CIF.
You can contact [email protected] to obtain download instructions of our package. Alternatively, you can also provide your input files so we would try out your structure here.
Oleg
Oleg Borbulevych, Ph.D.
Staff Scientist
QuantumBio, Inc.
2790 W. College Ave.
State College, PA 16801
E-mail: [email protected], [email protected]
Linkedin Professional Profile: http://www.linkedin.com/pub/oleg-borbulevych/22/454/b80
-----Original Message-----
From: "Maike Bublitz"
Sent: Monday, February 27, 2017 12:45pm
To: "Tanner, John J."
Cc: "[email protected]"
Subject: Re: [phenixbb] Phenix.refine ignores ligand planarity restraint
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thanks for the suggestion - I’ve tried both 0.001 and zero, as yet without success.
/Maike
On 27.Feb 2017, at 17:12 , Tanner, John J. mailto:[email protected]> wrote:
You could try setting the deviation from planarity parameter to a very small value (maybe zero?). It is the number after the atom name:
NAP plan-1 C6A 0.020
On Feb 27, 2017, at 11:05 AM, Maike Bublitz mailto:[email protected]> wrote:
Dear all,
this has probably been discussed many times before, but I just can’t seem to find a solution for my current problem with phenix.refine:
I am trying to refine a protein structure with a rather complex ligand. I’ve generated a .cif file for the ligand with eLBOW, including planarity restraints for its aromatic ring systems. However, phenix.refine keeps on distorting the 6-ring in my indole group, although all respective atoms are included in the plane definition.
At a resolution of 3.0 A, I’d very much prefer to impose an ideal planar structure on this ligand.
How can I convince Phenix to not distort my ligand's aromatic rings?
Many thanks for your kind suggestions.
Best regards,
Maike
*************************************************
Dr. Maike Bublitz
Associate Professor of Microbial Biophysics
Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU
United Kingdom
phone: +44 (0)1865 613221
lab: +44 (0)1865 613318
maike.bublitz(at)bioch.ox.ac.ukhttp://bioch.ox.ac.uk/
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