The keyword script Eckhard mentioned did the job I wanted to achieve. I
created the cif file for my ligand through the Monomer Library Stetcher
and then edited torsion angle part to include the restraint for the OH
tiling angle. I am running the CCP4 Suite 6.0.2 and CCP4i 1.4.4.2.
but I still have to include an external keyword script
restr tors include resi XXX
to impose torsion angle restraint on the ligand. With the script read in I
can further adjust the Overall wt for Torsion under Geometric parameters
menu to achieve a geometry that best fits to the density.
I have tried weighting term 0.05 or 0.08 for this case. The smaller weight
at 0.05 gave me better planarity for the aromatic residues without
sacrifying too much in R/R-free (only 0.1% lower with 0.08 weight).
Thanks again for suggestions from many others.
Huiying
On Fri, 5 Dec 2008, Eckhard Hofmann wrote:
Hi Huiying,
could you tell us which version of refmac you are using?
There has been an issue with torsion definitions in ligands NEVER included in
the refinement, even if they were in the cif (at least up to
Refmac_5.2.0019). I did have the same effect you had and wondered why. (See
list in October 2007)
Garib modified the code in a later version of 5.4 to allow you to include all
torsions from one residues by applying the following line:
restr tors include resi XXX
or to include only one specific definition in refinement
restr tors include resi XXX name var_1
In CCP4i you'll have to include this with the Developers Option to include an
external keyword-file. NOTE: Without doing anything, the torsion definitions
are still NOT used, which would explain the behaviour you observe. This is a
feature, not a bug ....
I'am not sure what the situation is in the current version, maybe Garib
should answer this?
Hope that helps,
Eckhard
Huiying Li schrieb:
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]
