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-restraints

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 <osobolev@lbl.gov> 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 <cpmasmit@gmail.com> 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.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

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