As already suggested you should use NCS averaging, but I would go the Parrot way http://www.ccp4.ac.uk/html/parrot.html or DM using a mask for your monomer of the hexamer and first ignoring the peptide. Do you have a ring or a dimer of trimers ? If however your two peptides follow NCS as well you might define a separate NCS operator for two-fold averaging of the peptide.
The improved map can then be exposed to Buccaneer (http://www.ysbl.york.ac.uk/~cowtan/buccaneer/buccaneer.html) for extension of your current model and possible automatic fitting of your two peptide chains. Jürgen On Apr 3, 2012, at 9:37 PM, 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 ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
