[phenixbb] phenix.refine and torsion-angle ncs

[Jeff Headd]

Hi Tony,

It is not necessary to exclude residues when using the torsion angle NCS
restraints, even if they are in different rotamers. The potential used to
restrain related torsions automatically shuts off in cases where the
related torsions are sufficiently different, such as for different
rotameric states.

If you want to firmly exclude them, you can define all your NCS groups such
as:

refinement {
  ncs {
    torsion {
      restraint_group {
        selection = chain A and resseq 1:50
        selection = chain B and resseq 1:49
      }
    }
  }
}

or something similar for your specific case. If you do define your groups,
you have to make sure you define enough groups to cover your entire model.

Jeff

On Thu, Jun 21, 2012 at 2:54 AM, Antony Oliver
<Antony.Oliver at sussex.ac.uk>wrote:

>   Dear phenix.bb
>
>  How do I specifically exclude particular amino acids from torsion-angle
> ncs?
> From the GUI, it is not obvious.
>
>  In a couple of my chains, one or two amino acids are in definite crystal
> contacts, and are therefore in a different rotamer/conformation compared to
> the other ncs-related copies.
>
>  Unfortunately, I can't seem to find the right option / keyword to stop
> the refinement job moving these side-chains to agree with the rotamers
> found in the other molecules of the asymmetric unit.
>
>  Many thanks,
>
>  Tony.
>
>
>   ---
>  Dr Antony W Oliver
>
>  Senior Research Fellow
>  CR-UK DNA Repair Enzymes Group
>  Genome Damage and Stability Centre
>  Science Park Road
>  University of Sussex
>  Falmer, Brighton, BN1 9RQ
>
>  email: antony.oliver at sussex.ac.uk
>  tel (office): +44 (0)1273 678349
>  tel (lab): +44 (0)1273 677512
>
>
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>
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