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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
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