[phenixbb] ncs

Maia Cherney chern at ualberta.ca
Tue May 5 16:16:24 PDT 2009


Thank you, Dale.
To clarify the 2 restraint groups for DNA, I meant two types of DNA 
sequences as the DNAs are double stranded; due to 3-fold there are 
totally 6 strands.


Maia



Dale Tronrud wrote:
>    If you have nearly C3 ncs symmetry parallel to the crystallographic
> 3-fold, you very likely also have some form of pseudo-translational
> symmetry.  If present this will lead to quite a few of your intensities
> being very small, and poorly measured.  This situation can require you
> to continue restraining ncs even at 2.1A resolution, particularly if
> many of your weak reflections are "unobserved".
>
>    It is quite possible that the free R is telling you exactly what
> you need to know, that your structure factors alone are insufficient
> to define your model.
>
>    Dr. Echols' comment:
>
>   
>>> It may be possible that the NCS restraints are biasing your test set,
>>> leading to the suspiciously low Rfree-Rwork gap, but I thought this
>>> only applied when the NCS approached crystallographic symmetry, and
>>>       
>
> is the reverse of my understanding.  The cross-talk between the working
> set and test set is minimal when the ncs approaches crystallographic
> symmetry, and at its worst when the two are unrelated.  When the ncs
> and "cs" are similar the ncs images of a test set reflections falls
> very near its proper symmetry images, which are also in the test set by
> definition.  When the two types of symmetry are unrelated, the ncs image
> of a test set reflection will fall near a reflection which only has a
> 5% chance of being in the test set.  Now you have a direct relationship
> between a reflection in the test set and one in the working set.
>
>    With care, a test set can be selected that minimizes this crosstalk.
> Since you have ncs symmetry that is masked by cs symmetry this is not
> much of a problem for you.  (I don't quite understand how the 2 copy
> ncs of the DNA relates to the crystallographic symmetry, so it might
> be a problem.)
>
> Dale Tronrud
>
>
>
> Maia Cherney wrote:
>   
>> Thank you Nat, Pavel,
>>
>> Actually, the NCS approaches a 3-fold crystallographic symmetry axis 
>> with 3 types of protein molecules plus 2 restraint groups for DNA molecules.
>>
>> The result is the same with "optimize_wxc=true optimize_wxu=true" 
>> options, Rfree is going up without NCS by ~1.5%. Rwork is practically 
>> the same.
>>
>> Should I increase the test set (now it's 5%)? or should I leave NCS=true 
>> for the final pdb?
>>
>> Maia
>>
>>
>> Nathaniel Echols wrote:
>>     
>>> On May 4, 2009, at 6:48 PM, Maia Cherney wrote:
>>>   
>>>       
>>>> The resolution is 2.15 A. The NCS was always on during the refinement
>>>> until we got low R factors (19.2% and 21.2%). Then the NCS was turned
>>>> off for the final refinement and the R factors increased, which is
>>>> strange as they should be going down when you apply less restraints.
>>>>     
>>>>         
>>> This isn't necessarily true - regardless of which program you use to  
>>> refine, R-work isn't actually the refinement target, and minimization  
>>> algorithms aren't foolproof either.  When you remove the restraints  
>>> you are effectively decreasing the observation:parameter ratio, which  
>>> increases the risk of overfitting.  If nothing else I would expect the  
>>> gap between Rwork and Rfree to increase, but I've also seen both  
>>> increase when NCS restraints were removed.
>>>
>>> It may be possible that the NCS restraints are biasing your test set,  
>>> leading to the suspiciously low Rfree-Rwork gap, but I thought this  
>>> only applied when the NCS approached crystallographic symmetry, and  
>>> there's no such thing as fivefold crystallographic symmetry.   
>>> Hopefully someone else on the list can clarify this.
>>>
>>> -Nat
>>>
>>> -------------------
>>> Nathaniel Echols
>>> Lawrence Berkeley Lab
>>> 510-486-5136
>>> NEchols at lbl.gov
>>>
>>>
>>>
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>>>   
>>>       
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