[phenixbb] modelling a flexible peptide

[intekhab alam]

Hi All
I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt
60 and 8 Kda respectively.
Molecular repalcement (60Kda protein as template) with Phaser gave a
solution with 6 molecules in ASU.
A continuous density is also obersved near two different chains which i
consider as the second protein.
I refined the density using a poly Alanine model but still i can't
recognise the side chains confidently for modelling.
Considering the fact that the smaller protein partner is rich in lysine,
arginine, Asp and Glutamate with only 3 tyr and 4 phe,
i tried to modell fragments one by one but the B-factor of the segments are
quite high (in the range of 110)
what will be the best strategy to improve the map for modelling.

regards

-- 
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
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