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Modeling of side-chains onto membrane ab initio cluster?

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Modeling of side-chains onto membrane ab initio cluster?
#1

Hi all,

I am running a big membrane ab initio calculation and clustering right now. So far everything ran well, and clustering gave me good results.

Now I want to remodel the best cluster into a full structure with amino acid side chains and so on. So I'm searching for an application in Rosetta, that can generate a full structure out of the low-resolution centroid models? As far as I know the original ab initio application switches between centroid modeling and refinement, so it should be possible to complete this task.

thanks a lot,
akfried

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Thu, 2011-06-23 04:03
akfried

I believe the relax executable is used for this purpose.

Thu, 2011-06-23 06:42
smlewis

The manual indeed states that it can read centroid models. Thank you!

Sat, 2011-07-02 15:15
akfried

hi akfried, could you please go through with me the steps you used for your membrane ab initio calculation and clustering? i have a 97aa membrane protein that i want to perform membrane ab-initio on.

your help is greatly appreciated.
thanks.

Sat, 2011-07-23 14:34
nkemjika