[phenixbb] modelling a flexible peptide

[Randy Read]

Hi,

Assuming that the smaller protein is in the same conformation in all 6 copies, 6-fold averaging should be very powerful.  If you already have a polyAla trace then the averaging will have a good mask to work from.  Even at 3A, maps with nearly perfect phases show a lot of detail (cf. maps from virus structures after averaging).

Averaging will work best if the 6 copies are in different orientations.  It won't work as well if the copies are related by pure translations (indicated by big non-origin peaks in the native Patterson map) or if the crystal is close to possessing some higher symmetry.

Best wishes,

Randy Read

On 4 Apr 2012, at 02:43, intekhab alam wrote:

> 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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> phenixbb at phenix-online.org
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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