[phenixbb] NCS operators

Jeff Headd jjheadd at lbl.gov
Mon Mar 19 21:37:20 PDT 2012

Hi Melania,

When you say you have one domain that is related by 3-fold symmetry and one
related by 6-fold symmetry, are each of these domains independent chains?
Or are these sub-domains of a single chain?

The torsion NCS restraints should work correctly if the domains are
independent chains. If not, it will take some parameterization.

The first thing to try will be to run:

mmtbx.find_torsion_angle_ncs_groups model.pdb

This command will output what the torsion NCS routine finds for NCS groups
by the automated method. If this gives you the NCS groups that you are
after, then all you need to do is add two options to your parameter file
(or turn these options on in GUI):

main.ncs=True ncs.type=torsion

If you are not getting the NCS groups that you would like, it is possible
to specify them by hand with:

ncs.torsion.restraint_group {
  selection = 'chain A'
  selection = 'chain B'

ncs.torsion.restraint_group {
  selection = 'chain C'
  selection = 'chain D'


If you'd like me to take a look at your file and see how the torsion NCS
code is interacting with it, I'd be happy to.


On Mon, Mar 19, 2012 at 7:54 PM, Paul Adams <pdadams at lbl.gov> wrote:

> Hi Melania,
>  I second Ralf's suggestion of trying the torsion NCS. I'm sure Jeff will
> say more, but it is very easy to use.
>  Cheers,
>        Paul
> On Mar 19, 2012, at 6:54 PM, Melania Strycharska wrote:
> > Dear all,
> >
> > I have a bit of a problem applying NCS to my fairly low resolution
> structure. If I try to look for NCS symmetry automatically - phenix doesn't
> find any. If I specify sections that I want to be related by NCS, the
> script usually crashes.
> >
> > I have a dimer in the asymmetric unit, however it appears that one
> domain is related by 3-fold symmetry while the other is related by 6 fold
> symmetry. I can "cheat" phenix and generate operators for each of the
> domains by feeding a stripped pdb file (one that contains only a dimer of
> one domain or the other) to phenix.simple_ncs_from_pdb and then it easily
> identifies the ncs operators... unfortunately the simple_ncs_from_pdb.ncs
> file generated that is meant to be fed into phenix.refine contains only the
> chain selections, not the actual operators.
> >
> > Is there a way to specify different NCS operators (rotational matrix and
> translational vector) for specific chain selections in the .eff file or
> under GUI? or if there isn't, how can I still take advantage of my NCS
> symmetry?
> >
> > Also, is there any obvious reason why NCS operators that I generated
> with Phenix do not match the operators that I found using CCP4 Lsqkab? (yes
> I already accounted for chain A moving onto B or chain B moving onto A)
> >
> > Can I choose to apply NCS symmetry to just my backbone? How would I
> specify that?
> >
> > thanks so much!
> > Melania
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> --
> Paul Adams
> Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley
> Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley
> Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Laboratory Research Manager, ENIGMA Science Focus Area
> Building 64, Room 248
> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> http://cci.lbl.gov/paul
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
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