Re: [phenixbb] keep torsion restraint on ligand

Hi Charles, you are right: setting very low esd is not good, and setting it to zero will disable the restraint completely. Pavel On 6/17/15 07:45, CPMAS Chen wrote:

Thanks, Oleg.

1 or 2 degrees work. Actually, it is in the FAQ of phenix refinement. Here is the page in case anyone else like to do similar restraint.

http://www.phenix-online.org/documentation/faqs/refine.html#targets-and-rest...

*I want my ligand geometry to be absolutely perfect with no deviation from the target value(s). Can I just set the sigmas to zero or an extremely low value?*

You cannot set the sigma to zero because the weight on the restraints is equal to 1/sigma^2. A very low value will not crash, but it will almost certainly confuse the minimizer and result in a sub-optimal structure, because those restraints will dominate the target and gradients, forcing the minimizer to take inappropriately large steps.

Charles

On Tue, Jun 16, 2015 at 1:12 PM, Oleg Sobolev mailto:[email protected]> wrote:

Dear Charles,

First of all, I would recommend to change value_angle_esd from 0 to something like 1 or 2 degrees if you want it to be tight. Next, make sure that your restraint is actually applied by inspecting the resulting .geo file and locating respective "dihedral" restraint.

Best regards, Oleg Sobolev.

On Tue, Jun 16, 2015 at 6:28 AM, CPMAS Chen mailto:[email protected]> wrote:

Hi, All Phenix Users,

I am fitting 2-bromoethanol to the density map. I want to keep its gauche conformation, so I edited the cif for this ligand to restrain the torsion angle,

loop_ _chem_comp_tor.comp_id _chem_comp_tor.id http://chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period BRJ Var_01 BR1 CB CB1 OB1 -60.00 0.0 3

But, after refinement, this angle can be close to 90 or even 120. Even worse is that the fitting at such angles are not better than at -60/60 angle.

How could I fix/restrain the angle during refinement?

Thanks!

Charles

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

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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