[phenixbb] Phenix.refine ignores ligand planarity restraint

Tue Feb 28 11:41:16 PST 2017

Maike

One more word of advice. Try to provide eLBOW with as much information as
possible. Your restraints file showed that you had used a PDB file input
without, I assume, hydrogens. A SMILES string is a better choice as it has
a higher chemical information content.

BTW, Phil Jeffrey is correct that zero esd turns off the restraint. Also,
making the esd too small is also not advisable. For example, a plane esd of
0.02 is fine, but 0.002 may be too small. As a rule of thumb, don't make
the esd more than 10x smaller than the default.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Feb 28, 2017 at 11:30 AM, Maike Bublitz <
maike.bublitz at bioch.ox.ac.uk> wrote:

> Dear all,
>
> as it turns out, the cif file was just fine after I had defined the planes
> properly.
> I was just accidentally using a script in which I had switched off
> coordinate refinement. D’Oh. My desk has a bite mark now.
>
> Thanks, Pavel, for spotting this, and thanks to all for your suggestions.
>
> Cheers,
> Maike
>
>
>
>
>
> On 28.Feb 2017, at 17:13 , Pavel Afonine <pafonine at lbl.gov> wrote:
>
> 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> <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> <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/><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 <+44%201865%20613221>
> lab: +44 (0)1865 613318 <+44%201865%20613318>
> 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 <+44%201865%20613221>
> lab: +44 (0)1865 613318 <+44%201865%20613318>
> maike.bublitz(at)bioch.ox.ac.uk
>
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