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Abinitio Calculations - typical parameters

Dear all,
I am using rosetta for abintio calculations for a while now. I am curious to know what are other parameter other than mentioned in the documentation, to play with to simulate protein size of 150 aminoacids. I am not really satisfied with the results obtained with typical parameters and wondering my laptop took only like one hour to complete the job ( but heard previously it is computationally intensive process)

Here is my flag file
-database /home/vamsi/Programs/Rosetta31/rosetta_database/
-in:file:fasta inputs/t000_.fasta

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relax with restraints

Hi there,

Is it possible to use the relax app to relax an structure while restraining the C-alpha coordinates to their initial positions in order to stop things blowing up? There seems to be an option -constrain_relax_to_start_coords but it doesn't appear to have much effect when I tried using it.

thanks for your help!

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Does Rosetta have homology modeling protocol?

Hi all,

Does Rosetta have a homology modeling protocol like SWISS-MODEL or MODELLER? I couldn't find it in source code.
I want to predict the structure of a sequence and then do a protein-protein docking, need I use MODELLER to create the structure from sequence and template pdb before repacking or loop modeling using Rosetta?


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Fundamental methods: pose.residue().total_atom(), pose.atom(#) ?

Are there any methods that can return the total number of atoms in the pose? I am trying to do a simple operation, like shift a peptide some distance along a certain vector, and find myself unable to loop over atoms in the simulation.

Is there a resource that lists all the methods accessible from the Rosetta python library?

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