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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?

Thanks.

Post Situation: 

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?

Post Situation: 

RosettaSnugDock-2.3.1 build Error!

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

$ 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!

Post Situation: 

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

Hi,

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

src/protocols/moves/SidechainMover.cc:158: error: 'const class core::scoring::dunbrack::SingleResidueDunbrackLibrary' has no member named 'get_phi_from_rsd'
src/protocols/moves/SidechainMover.cc:159: error: 'const class core::scoring::dunbrack::SingleResidueDunbrackLibrary' has no member named 'get_psi_from_rsd'
src/protocols/moves/SidechainMover.cc:186: error: 'class core::scoring::dunbrack::DunbrackRotamerSampleData' has no member named 'chi_probability'

Post Situation: 

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

 

Post Situation: 

error in installation

hi everyone

I am trying to install rosetta on ubuntu maverick (10.10) and having troubles with it .... I tried to install with a lower version of gcc-4.2 (as suggested in the installation guide) instead of the gcc-4.4 (default for maverick) but it is giving the same error at one file:

/src/core/scoring/sasa.cc: 618 internal compiler error: Segmentation fault

is there anyone facing the same problem or know anything about how I go about solving it .. please let me know

cheers
yogesh

Post Situation: 

Mac OSX installation

Hi everyone,

Here I'm sharing my frustration with using this module on Mac, with the hope of saving you some time, or finding a solution:

The library files (.so & dylib files) included in the package are ONLY compatible with the python 2.5 (and no other version) that is shipped with Mac OS.
This is a serious problem as many basic modules (e.g. numpy & scipy) are not compatible with this python and require standard version of python from python.org.
Here are some tricks that didn't work:

Post Situation: 

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