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.
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]
