On 28.Feb 2017, at 19:41 , Nigel Moriarty <[email protected]> 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 BioimagingLawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Tue, Feb 28, 2017 at 11:30 AM, Maike Bublitz <[email protected]> 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 <[email protected]> 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 <[email protected]<mailto:[email protected]> > 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 [email protected]< mailto:phenixbb@phenix-online. http://phenix-online.org/org> mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave@phenix-online.org _______________________________________________ phenixbb mailing list [email protected]< mailto:phenixbb@phenix-online. http://phenix-online.org/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>
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************************************************* Dr. Maike BublitzAssociate Professor of Microbial BiophysicsDepartment of BiochemistryUniversity of OxfordSouth Parks RoadOxford OX1 3QUUnited Kingdomphone: +44 (0)1865 613221lab: +44 (0)1865 613318maike.bublitz(at)bioch.ox.ac.uk
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