[phenixbb] NCS, TLS and anisotropic b-factors

Morten Groftehauge mortengroftehauge.work at gmail.com
Tue May 8 07:45:50 PDT 2012

Okay, brilliant. I had a base go off the rails with B-factor and it's NCS
mate got weird positive difference density. So I instantly looked for stuff
in the manual to explain it. Like I said it was a stupid question =)

On 8 May 2012 12:08, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Morten,
> So what is the correct way of handling TLS and NCS?
> nothing special. Just ask phenix.refine to use TLS (define TLS groups or
> ask phenix.refine to find them automatically - this is very quick, may take
> a minute or less), and also ask phenix.refine to use NCS restraints.
> For NCS restraints you have two options: use Cartesian or torsion NCS. For
> Cartesian NCS you can let phenix.refine find groups automatically (the
> algorithm is not very smart though) or provide your atom selections for NCS
> groups yourself.
> For torsion NCS you don't have to do anything; and this is the recommended
> option.
> A very simplistic example using command line (sure, all this is available
> in the GUI !):
> phenix.refine model.pdb data.mtz
> strategy=individual_sites+individual_adp+tls main.ncs=true ncs.type=torsion
> tls.find_automatically=true
>> On the phenix website it says under *current limitations of phenix.refine
> * "Atoms with anisotropic ADP in NCS groups". I take this to mean that
> phenix.refine doesn't handle the combination of TLS and NCS well, is this
> correct?
> Sorry for this not being clear enough. All it's trying to say is that if
> you refine individual ADPs, NCS restraints will not handle B-factors
> correctly because NCS matrices should be applied to ADP matrices before
> applying similarity restrains. This is not implemented.
> However, this is never realistic situation: if you refine with individual
> anisotropic ADPs then you never need to use NCS, and the other way around
> is true too. If you use TLS, then NCS are applied to residual (local atomic
> ADPs) only, so it's not a problem as well.
> Pavel
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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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