[phenixbb] keep torsion restraint on ligand

CPMAS Chen cpmasmit at gmail.com
Wed Jun 17 07:45:29 PDT 2015


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> 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> 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
>> _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
>>
>> ******************************************************
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>
>


-- 

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

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

******************************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150617/2ba98a1d/attachment.htm>


More information about the phenixbb mailing list