Hi all

I have a 3A dataset for a protein-protein complex. I have successfully build the first protein and refined it to R/Rfree 24/28. I can see some density for my second protein but the density is a bit noisy. I have attached the coot image of the density.  I want to model the aminoacid having sequence as given 

1.Based on map features which segemnt should i start with.

2. Is there anyway that i can  build the best fit segment of my second protein. 

I tried autobuild but it failed to build any peptide for my second protein.

 

Your help is highly appreciated.

 

regards

 

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INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL