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How to relax a protein model calling Rosetta functions from my C++ code

My code creates protein models that need to be relaxed in order to lower their energy as these models may have some close contacts and other non-protein like features. According to the online documentation, the Rosetta command for relaxing non-idealized structures is
rosetta.exe aa xxx_ -relax -farlx -minimize -s xxx.start -fa_input -fa_output -use_input_bond

My questions are: 1) Is this the correct command for relaxing my models and make them "fall" in the nearest local minimum? 2) If so, how can I call these functions from inside my C++ code?

Post Situation: 

Error while running Enzyme Design

Hello,
I am attempting to use the Enzyme Design application to redesign a ligand binding site to accept a different ligand. I am running the following command:

$ROSETTA33/bin/enzyme_design.linuxgccrelease -database $ROSETTA33/rosetta_database -in:file:s input.pdb -in:file:extra_res_fa LG2.cen.params LG2.fa.params LG1.cen.params LG1.fa.params -enzdes:cstfile constraints.cst -enzdes:detect_design_interface -enzdes:cst_design

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Selecting Top Scoring Decoys

Hi

I have a silent file of 20,000 decoys and I want to extract/separate low energy decoys out to a separate silent file for all atom relax. Is there any possibility of doing it. I tried cluster.linuxgccrelease with -cluster:output_score_filter and it doesn't seem to work! Is there any workaround or possibilities of any script!

Post Situation: 

ld: cannot find -lz

Dear colleagues,

I am trying to install Rosetta 3.3 on:

- HP ProLiant DL380 G6
- CPU: 2 x Intel Xeon Quad Core
- OS = SUSE SLES 11, kernel 2.6.27.19, x86_64
- compiler: gcc 4.3-62.198-x86_64
- python: 2.6.5
- scons: 2.1.0

command: scons bin mode=release

crash + error message:

/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm

Post Situation: 

PyRosetta Initial Setup

Mac OSX 10.7 - Lion 64bit
Python v2.7.2
PyRosetta 2.0

I downloaded and extracted the files for PyRosetta. I moved them to my documents. When I open terminal and go the directory where PyRosetta is located I cannot step 4 to work from the instructions online.
"
4. From within the PyRosetta directory, type 'source
SetPyRosettaEnvironment.sh' into the command line to set up the PyRosetta
library filepaths"

I type "bash-3.2$ source SetPyRosettaEnvironment.sh"

I receive an error that says "bash: cd: SetPyRosettaEnvironment.sh: not a directory

Post Situation: 

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