[phenixbb] Setting up MR_Rosetta

Julio Lenin jdoming at ucdavis.edu
Sun Nov 4 15:13:17 PST 2012

Hello guys,

I am currently trying to setup MR_Rosetta but I am running into some trouble. When I run the tutorial for Defensin HNP-3 from the GUI I always get an error during the ... process (see image at this dropbox link). I know that my path for phenix and rosetta are correct since I can run the phenix_regression.wizards.test_command_line_rosetta_quick and phenix_regression.wizards.test_command_line_rosetta_quick test_rosetta_rebuild. If I try to trace down the error, I can only get the same info that I got from the GUI error message (vide supra). 

As additional info, here are somme details of my setup:

MacBookPro 4,1 running OS 10.6.8
Core2Duo 2.5 Ghz
6 Gb RAM
Rosetta 3.2 compiled with flags bin mode=release
Phenix 1.8.1-1168

And my input settings for the GUI run (dropbox)

Now, this might just be confusing but there was one command line test that my setup failed: phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta

The error is kinda cryptic (see dropbox copy of the error) but it seem to be a discrepancy in the scoring results not a missing program or any other kind of misconfiguration. Of course, I might be wrong. 

Any advice?

Best regards. 

Lenin Domínguez-Ramírez

"And for all the current and rather silly emphasis on structural   
biology,understanding enzymes means understanding catalysis and   
catalysis is concerned with kinetics, not structure: as Jeremy   
Knowles aptly remarked, studying the photograph of a racehorse cannot   
tell you how fast it can run." 
Cornish-Bowden, 1995

Lenin Domínguez-Ramírez, PhD 

"What are we to think of an organism that loses practically all of its cellular water at ordinary temperatures and pressures and ceases to metabolize, but upon being rehydrated resumes all of the characteristics it previously exhibited?...we should be reluctant to call such an organism dead (unless we are willing to entertain the possibility of its resurrection) because it resumes an active life upon simple restoration of water."

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