[phenixbb] NCS operators

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Mon Mar 19 19:16:25 PDT 2012

Hi Melania,

> 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.

What is the error message?

> 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.

The operators are recomputed each time the NCS is used, based on the
current coordinates. There is not way to enter the operators externally.

> 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)

Not sure.

> Can I choose to apply NCS symmetry to just my backbone? How would I
> specify that?

For example:

selection = "chain A and backbone"

You may want to try Jeff's new torsion angle NCS, which often gives better
results than the Cartesian NCS and is very easy to use. I hope Jeff will
chime in.


P.S.: You probably figured this out already: you want to set
ncs.find_automatically=False if you give you own selections for Cartesian
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