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
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