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]
