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

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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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.


 Hmmm - 50A is quite low anyway - is it complete and well measured?

Many viral capsids contain spherically averaged RNA - it is quite rare
to see a good image, especially in a high symmetry spacegroup - the RNA
may very well NOT obey the same symmetry operators..

>    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?


 REFMAC5 automatically does this - you should run the uniquify script to
make sure you have generated a complete set of hkls and assigned FreeR
flags as required. (ask if you dont know how to preserve and extend the
existing set - but if you type
uniqueify without any parameters you get some instructions..)
However dont be disappointed if it doesnt help much!

 Eleanor