[phenixbb] Refining with NCS

Pavel Afonine PAfonine at lbl.gov
Mon Aug 25 11:57:47 PDT 2008

Hi Kate,

one can endlessly talk about this matter and there is a number of good 
papers out there. 

At some point I spent significant amount of time trying to address the 
questions you mention below. I selected all structures from PDB for 
which NCS is available and re-refined them with and without NCS. My goal 
was to answer this question: given a model and data, can I tell for sure 
if I need to use NCS or it's better to refine without using NCS. In the 
end I couldn't derive any reliable formula to be able to decide if I 
need to use NCS or not. All I re-discovered was the old and well known 
fact: if have have NCS, then lower the resolution, more likely you want 
to use NCS -:) Obviously, at ~1.5A resolution the use of NCS was only 
damaging. And ~2.0A is kind of "gray area".

So this is why I wrote in my previous email that it is much easier, 
quicker and reliable to just try both ways and see which one works 
better, rather than waste time on speculating -:)


On 8/25/2008 11:33 AM, Kate Kavanagh wrote:
> I was wondering if there a consensus of when it is mandatory to use ncs 
> in refinement. Is is dependent on:
> 1. resolution?
> 2. data-to-parameter ratio?
> 3. difference between Rcryst & Rfree?
> 4. something else...
> Or does one just do as Pavel states and try both ways ?
> Regards,
> Kate
> Pavel Afonine wrote:
>> Hi Francis,
>>> Also if anyone has a paper/protocol for NCS refinement, I'd love to  
>>> check it out (to figure out which map to fit to).
>> Just something to keep in mind... I always prefer to run two refinements 
>> in parallel with and without using NCS. It's resolution (and 
>> data-to-parameters ratio) dependent. I've seen a  number of cases where 
>> using the NCS is very beneficial and similar number of cases where it's 
>> better to not use NCS (mostly at resolutions ~2-2.5A).
>> I would also check manually the NCS groups that are found by 
>> phenix.refine automatically. I have some cases where automatic detection 
>> did not yield a good selection.
>> Pavel.
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