unidentified density

From: intekhab alam
Date: 10 February 2012 07:35

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
--
INTEKHAB ALAM

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From: Tim Gruene

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
- --
- --
Dr Tim Gruene

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From: Eleanor Dodson

Try buccaneer - it should work very easily with that density..
Eleanor

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From: intekhab alam


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