Acturally, I want to find a way to keep the OH tilted out of the
neightbouring plane by about 10 degrees. At 2.1A resolution the REFMAC
refinement tends to refine it into the plane even though I have included
torsion angle restraint in the library for the ligand. I thought I could
play with the weight or the esd of the target value but having trouble to
achieve it. In CNS, adjusting the force constant of the target value is a
way to tighten or loosen the restrain. I would like to know how to
"enforce" a geometry effectively in REFMAC.
Thanks for any comments.
Huiying
On Wed, 3 Dec 2008, Abhinav Kumar wrote:
> If you want to restrain the OH group to a plane, you need to include it in
> the plane definition, and not the torsion definition.
>
> Thanks Abhinav
> Stanford Synchrotron Radiation Laboratory Joint Center for Structural
> Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292
>
>
> Huiying Li wrote:
>> I want to impose restraints during REFMAC refinement on the tortion angles
>> that control the tilting of an OH group from a plane in a ligand bound to
>> the protein. A few things that confused me:
>>
>> 1. In library cif file, should I just increase or decrease the
>> tor.value_angle_esd if I want to loosen or tighten the restraits?
>>
>> 2. What is the meaning of the last column in torsion angle parameters:
>> _chem_comp_tor.period, in cif file? In the PDB output file REFMAC also
>> lists the RMS and WEIGHT for the torsion angles, period 1 through 4.
>>
>> 3. In REFMAC gui under Geometric parameters, there is only one user
>> controlled weight for torsion. By changing the weight here, does it change
>> the torsion weight for all 4 periods?
>>
>> Thanks in advance for the help.
>>
>> Huiying
>
--
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
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