It is worth doing sme rounds of non-NCS restrainded refinement then
sending it to the Ethan Merrit server to get TLS groups suggested..
Eleanor
Frank von Delft wrote:
> Two points:
>
> 1. B-factors tend to differ lots between NCS copies, so you want to
> set those restraints rather low (at least, I always do, by default)
>
> 2. NCS groups tend to need a far more fine-grained description than
> just plonking in the whole domain. For structures in my lab, we often
> see that tight NCS "does not work" -- until the group definitions are
> selected more carefully.
>
> Cheers
> phx
>
>
>
> Nicholas Keep wrote:
>> I am refining a low (3A) resolution structure of a 3 domain protein.
>> There are 4 copies in the ASU. I have been applying tight NCS
>> restraints by domain in refmac and have pulled the weak MR solution
>> down to Rfree below 30 (just).
>>
>> However my question is that in 2 of the 4 copies one of the domains
>> is very poorly resolved. I can lower Rfree by around 0.5% by
>> omitting the domains from the PDB entirely or not applying the NCS
>> restraints to these copies of the domain. Clearly they are there and
>> should resemble the moderately well resolved copies by coordinates
>> but the way Bfactor restraints are applied between NCS copies seems
>> to be the issue. If tight restraints are included the B factors are
>> much lower (30-40) rather than 60-80 for the poor domains.
>>
>> I was wondering if there is a theoretically correct way to treat this?
>>
>> Would applying TLS scaling to each domain lead to the residual B
>> factors being more balanced?
>> Can a B factor offset be applied to the NCS restraints or could I
>> only apply a coordinate restraint not a B factor restraint between
>> certain copies?
>>
>> Comments welcomed especially from Garib.
>>
>> Happy New Year
>> Nick
>>
>>
>>
>>
>>
>
>
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