[phenixbb] Phenix.refine ignores ligand planarity restraint

[Nigel Moriarty]

Maike

That is a reasonable approach. Having a well minimised geometry with
hydrogens has all the right ingredients.

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 11:49 AM, Maike Bublitz <
maike.bublitz at bioch.ox.ac.uk> wrote:

> Dear Nigel,
>
> thanks for pointing this out. I had actually given eLBOW a pdb model of
> the ligand with hydrogens. This model came out of maestro, where I had
> built and energy-minimized it.
> In that cif file you saw, I had deleted all the hydrogens later on,
> because the ligand in my refinement complex didn’t have any, and in my
> desperation I thought that might be a problem.
>
> Best,
> Maike
>
>
> On 28.Feb 2017, at 19:41 , Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
>
> 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 <(510)%20486-5709>     Email : NWMoriarty at LBL.gov
> <NWMoriarty at lbl.gov>
> Fax   : 510-486-5909 <(510)%20486-5909>       Web  : CCI.LBL.gov
> <http://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 <+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/><http://bioch.ox.ac.uk> <http://bioch.ox.ac.uk/>
>>
>>
>>
>>
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>>
>>
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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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>
>
> *************************************************
> 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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