On Thursday 04 December 2008 11:50:30 Huiying Li wrote:
> Thank you all for suggestions and explanations. I did not make it clear. The
> tilt angle I wanted to restrain is the one from a C-OH bond to a plane
> (The C is in the plane). The O atom of OH group is not in the planar
> restraint in the cif file. At 2.1A I can "see" the feature of tilting of
> this OH group from the initial density map when the ligand was absent.
> But the density seems not strong enough to convince REFMAC that there is
> a tilt there. I have used very low weight term of 0.05 in the GUI to down
> weight the X-ray term. Refinement still pushed OH into the plane. I wonder
> if there are other tricks that can impose the restraint for this torsion
> angle.
From your description, it is still likely that a planarity restraint
is involved, rather than a torsion restraint.
Perhaps you should post the library *.cif file that you are using for this
compound.
Ethan
>
> Best,
> Huiying
>
> On Thu, 4 Dec 2008, Ian Tickle wrote:
>
> > Hi Huiying
> >
> > At 2.1A I would be very surprised if you see any density for the H atom
> > in which case the refinement is not going to move it out of the plane
> > whatever weight you give the torsion restraint. To answer your earlier
> > questions the period of a torsion restraint is the number of energy
> > minima in a complete rotation of the angle, so the OH bond will have a
> > period of 2, and
> > yes the same overall weight is applied to all torsions regardless of the
> > period, though individual torsions will also be weighted by 1/sd^2.
> >
> > Cheers
> >
> > -- Ian
> >
> >> -----Original Message-----
> >> From: [EMAIL PROTECTED]
> >> [mailto:[EMAIL PROTECTED] On Behalf Of Huiying Li
> >> Sent: 04 December 2008 16:35
> >> To: Abhinav Kumar
> >> Cc: CCP4BB@JISCMAIL.AC.UK
> >> Subject: Re: [ccp4bb] tortion angle restraints in REFMAC
> >>
> >> 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
> >> email: [EMAIL PROTECTED]
> >>
> >>
> >
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>
> --
> 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
> email: [EMAIL PROTECTED]
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
