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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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RosettaSnugDock-2.3.1 build Error!

$make gcc
Illegal variable name.
make: *** []

$ scons mode=release
KeyError: "Unknown version number 4.4 for compiler 'gcc'"
scons: done reading SConscript files.
scons: Building targets ...

How can I solve these problem? Could someone tell me! Thank you very much!

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Problem while unzipping the source code

I intend to install Rosetta version 3.1 for Windows. However problem started even at the time of unzipping the source rosetta3.1_source.tgz :-((

The warning message tells:
rosetta_source\ide\test\utility\pointer\ folder does not exist. Do you want to create it? on either yes or no it's terminating generating the following error message. The unzipping is incomplete and the Bin, Lib folders are empty

! C:\Documents and Settings\user\Desktop\myself\rosetta\rosetta3.1_source.tgz: Cannot open (.\src --> )

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Backrub patch


When I add the rosetta3.1_backrub_patch35535 rosetta can't compile.
It complains about the new

src/protocols/moves/ error: 'const class core::scoring::dunbrack::SingleResidueDunbrackLibrary' has no member named 'get_phi_from_rsd'
src/protocols/moves/ error: 'const class core::scoring::dunbrack::SingleResidueDunbrackLibrary' has no member named 'get_psi_from_rsd'
src/protocols/moves/ error: 'class core::scoring::dunbrack::DunbrackRotamerSampleData' has no member named 'chi_probability'

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error running rosetta3.1 demos

Hello, I compiled Rosetta3.1 on Ubuntu 8.2, the complie is fine no error report. Then I run some example under rosetta_demons/ directory according to the readme file in the directory, and I have errors:

for rosetta_demos/Ligand_Docking, the error is :

ERROR: Unable to open file: ./silent.out

ERROR:: Exit from: src/protocols/jobdist/JobDistributors.hh line: 825


for rosetta_demos/Docking, the error is:

ERROR: Option matching -dock_mcm not found in command line top-level context


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