Thanks to the members for responding to my queries. I would like to summarize the post as: 1.Improve the crystals to have a better dataset. 2. Poly A/G modelling to improve the density and then model the sequence. 3. use of secondary structure prediction tools and docking the sequence accordingly. 4. use of buccaneer.
i will post again once i get a reasonable model. regards intekhab alam On Fri, Feb 10, 2012 at 8:58 PM, Eleanor Dodson <c...@ysbl.york.ac.uk>wrote: > On 02/10/2012 07:35 AM, intekhab alam wrote: > >> 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 >> peptide: >> MGKKGKNKKGRGRPGVFRTRGLTDEEYDEF**KKRRESRGGKYSIDDYLADREREEELLERD** >> EEEAIFGDGFGLE >> >> 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 >> > > > Try buccaneer - it should work very easily with that density.. > Eleanor > -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
