-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hallo ,
first build a poly-ALA stretch. In coot or O this is conveniently achieved using baton-build mode. This should improve the phases. Then look at the side chains.Turbo-frodo has got somehting like a slider that shows the sequence on screen and which helps you identify bulky side chains. The pattern of a few bulky and non-bulkyside chains might already be sufficient to dock the sequence into the density. Also take the environment into account and think about what interactions between side chains of peptide and protein are plausible. You can also take the results from secondary structure prediction into account (e.g. http://toolkit.tuebingen.mpg.de/hhpred) - the density you show looks like an alpha-helix, and according to hhpred the stretch of sequence below contains two helices. Cheers, Tim On 02/10/2012 08:35 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: > MGKKGKNKKGRGRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLE > > 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 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPNOmBUxlJ7aRr7hoRArQMAJkBfnu04rQX2nBwgGN13qiwg68JzgCg0aL9 6C2LEaLZA37XVmQ+siX8yrg= =+AF/ -----END PGP SIGNATURE-----
