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@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     Email : NWMoriarty@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Feb 28, 2017 at 11:30 AM, Maike Bublitz <maike.bublitz@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@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>) 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@daletronrud.com<mailto:detBB@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>












_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org<mailto:phenixbb@phenix-online.org>
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org<mailto:phenixbb@phenix-online.org>
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org

*************************************************
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>

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org

*************************************************

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

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org

*************************************************

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