[phenixbb] Phenix.refine ignores ligand planarity restraint

Pavel Afonine pafonine at lbl.gov
Tue Feb 28 09:13:25 PST 2017


Excellent point! Have a look at *.geo file that lists absolutely all 
geometry restraints that are used in refinement (bonds, angles, 
torsions, planes, chirals, non-bonded, ncs, etc..). If the plane in 
question is not listed there then we will need to investigate why is that.

Pavel

On 2/28/17 09:01, Tim Gruene wrote:
> Dear Maike,
>
> did you read the log file to see whether any of your restraints get
> acknowledged by phenix.refine? There can be many reasons why they are not,
> e.g. mismatching atom names, mismatching residue abbreviation, ...
>
> Regards,
> Tim
>
> On Tuesday 28 February 2017 04:44:43 PM Maike Bublitz wrote:
>> Dear all,
>>
>> thank you again for all your suggestions. Here’s what I’ve tried, without
>> success:
>>
>> 1) reduce deviation from planarity restraints to very small value or zero
>> -> ligand still gets distorted in refinement
>>
>> 2) Set all bond angle restraints to ideal values and checked sums of angles
>> in planar rings -> ligand still gets distorted in refinement
>>
>> 3) Used phenix.elbow with - -final-geometry on a pdb of a planar ligand —>
>> ligand still gets distorted in refinement
>>
>> 4) Used the grade server
>> (grade.globalphasing.org<http://grade.globalphasing.org>) to generate cif
>> file from SMILES string—> phenix.refine stops with message “Unknown file
>> format: grade-ligand.cif”.
>>
>> Does anyone have another suggestion, except for installing an extra QM
>> package?
>>
>> Best,
>> Maike
>>
>>
>>
>>
>> On 27.Feb 2017, at 17:24 , Dale Tronrud
>> <detBB at daletronrud.com<mailto:detBB at daletronrud.com>> wrote:
>>
>>
>>    You could also check that the other restraints in your cif are
>> compatible with planarity.  If the sum of the three bond angles for a
>> planar atom is less than 360 deg your angle restraints will be fighting
>> with your planarity.  You also have to check the sum of the internal
>> angles of your planar rings.  If I recall correctly the sum of the
>> internal angles must equal n*180 - 360 for the ring to be flat.
>>
>> Dale Tronrud
>>
>> On 2/27/2017 9:05 AM, Maike Bublitz 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.uk<http://bioch.ox.ac.uk>
>> <http://bioch.ox.ac.uk>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>> *************************************************
>> 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.uk<http://bioch.ox.ac.uk>
>>
>>
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