Re: [ccp4bb]: missing low resolution caused Fourier ripples?

[William Scott <wgscott@chemistry.ucsc.edu>]

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This could be two problems.  The first is what you mention -- i.e., lack 
of low resolution data could make the map more broken up.
However unless the RNA inside shares the same noncrystallographic 
symmetry as the virus capsid, you will see an n-fold average of 
different lower symmetry structures, where n is the order of the NCS.  
This is most often the case.  The parts you do see are probably locally 
similar.


On Thursday, March 28, 2002, at 02:42 PM, Jinghua Tang wrote:

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>
>
>  Dear all,
>    I am working on a virus structure. The experimental observation
> contains data from 3.5 A to 50 A. From this data, I can see the virus
> protein capsid quite clearly. But when I try to look for anything in the
> RNA region in the center of the virus particle, I can only see some
> concentric shells of electron density at 1/3 of the protein level. As I
> understand that lack of enough low resolution infomation will generate
> Fourier ripples in the electron density map also with concentric 
> feature.
>    I am very grateful for any suggestion on how to differentiate the
> Fourier ripples effect and the real structure feature in the inside of 
> the
> virus.
>    Is it reasonable to use low resolution reflection calculated from the
> protein model to fill in the missing low resolution data to get rid of 
> the
> Fourier ripples effect? What CCP4 programs can be used to for this job?
>    Thank you in advance for any suggestion!
>    Jinghua
>
>
>