Using the SBGrid Environment
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Hardware Support Notes
Running PHENIX with Rosetta requires compatible versions of PHENIX and Rosetta to be installed and enabled in the shell environment. In the SBGrid environment, the default versions of Rosetta and PHENIX are compatible and tested. Other versions may also work together (nightly builds), but we don't typically test all possible combinations.
A quick check of PHENIX Rosetta integration can be made with the phenix_regression.test_rosetta_refine command.
A successful test will output this :
$ phenix_regression.test_rosetta_refine /programs/x86_64-linux/rosetta/3.8/main/source OK
phenix.rosetta_refine can be run from the GUI or from the command line.
We test rosetta with a small 61 aminoacid protein (1I2T, Poly-A binding protein, PABP). Our test dataset is available here : 1I2T.tar.bz2
This command should run to completion :
phenix.rosetta_refine 1I2T.pdb 1I2T_F.mtz protocol=hires nproc=8
Here is the expected log output. phenix.rosetta_refine.log