[phenixbb] refinement question

[Maia Cherney]

Francis, Engin,

Thank you very much for you input. I appreciate your idea to keep the 
ncs, but remove it from some parts of the model that have violations.

 Maia

Francis E Reyes wrote:
> NCS restraints increases the data:parameter ratio in low resolution  
> situations. Others have suggested not releasing NCS restraints unless  
> your resolution is > 2.0A and the model is complete (as including NCS  
> can help you build/complete your model with the use of NCS averaged  
> maps). When you do not include NCS, do you see sidechain differences  
> among the monomers making up the NCS?
>
> Personally I keep NCS in unless I do see genuine differences among the  
> monomers (which could be biologically significant depending on your  
> system). Of course these small differences (say in a binding pocket)  
> would likely need to be verified with omit maps or even better,  
> biochemically.
>
> Just my 0.02.
>
> FR
>
> On Jun 26, 2009, at 9:49 AM, Maia Cherney wrote:
>
>   
>> Hi all,
>> I am wondering why the ncs refinement gives me a better Rfree (21.0%)
>> than without ncs (21.7%). I have this experience with different  
>> projects
>> and different data  (3.3 A  and 2.3 A). The R work is similar ~18%
>>
>> As it's a fact with my data, which refinement do you think should be  
>> the
>> final?
>>
>> Maia
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>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
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