In addition to what the others have mentioned, if you're curious about sigma levels to contour you may want to deliberately omit

an atom from your structure (say an ordered oxygen in a good portion of the structure) - the height of the difference density peak would be meaningful and you then could roughly judge whether your other peaks are garbage or not.

 

Artem

On Wed, Jan 6, 2010 at 12:21 AM, Rajan <[log in to unmask]> wrote:

Dear All,

Happy New Year

I am working with a 2.06 Ang resolution structure in F432 space group and further using REFMAC (also tried Phenix) program for refinement of my model. 

Every thing in the structure seems good, R factor/ R free= 18.59/20.77 but the structure is too noisy (blobs of difference Fourier with red as well as green density).

As such electron density is looking good for the protein part.    

Is there any parameter which i had to check.

Thanking you in advance

Rajan

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Current Address:

Rajan Vyas
Research Scholar
Deptt. of Biotechnology
Panjab University Chandigarh, India
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