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  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

If not already tried we'd also suggest use of the torsion space NCS - in a recent nightly build. Jeff can say more about the modification of the ADP restraints in this case. Paul Adams Sent from my iPhone On May 8, 2012, at 10:55 AM, Nathaniel Echols wrote:

On Tue, May 8, 2012 at 7:45 AM, Morten Groftehauge wrote:

...

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 =)

One word of caution: the use of B-factor restraints on NCS-related atoms frequently makes structures much worse - Jeff and I have found lots of examples where chains have nearly identical conformations but wildly different B-factors. So you might want to experiment with setting the NCS B-factor weight to zero. (The reason this isn't the default is a) historical baggage, and b) where appropriate, it does help a little bit with overfitting.)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb