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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?

Thanks.

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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?

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!

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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

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'

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