[phenixbb] keep torsion restraint on ligand

[Pavel Afonine]

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-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 at lbl.gov 
> <mailto:osobolev at 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 at gmail.com
>     <mailto:cpmasmit at 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.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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