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Hi all,<br><br>I wanted to use the rebuilding feature of Rosetta to help improve the R-fators of MR solution in a new space group. I'm using Phenix 1.7.1-743 w/ Rosetta 3.2 on MAC OSX 10.5.8<br><br>installation was succesful, so after editing my .profile to include export PHENIX_ROSETTA_PATH=/usr/local/bin/rosetta, I tried to run the following tests:<br><br><pre>1. phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up <br><br>2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta <br><br>3. phenix_regression.wizards.test_command_line_rosetta_quick_tests <br><br>While the first was successful (<font style="" color="#0070c0">ALL COMMAND_LINE TEST OK</font>), the second reported the following error:<br><br><font style="" color="#0070c0">Error: test_command_line_rosetta failed</font><br><br>Upon subsequently running the test_mr_rosetta.com script created in the subdirectory, the following error was reported:<br><br><font style="" color="#0070c0">coords1.ali</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">coords1.pdb</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">fobs.mtz</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">mr_rosetta_quick.eff</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">perfect.mtz</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">seq.dat</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">test3.gz</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">test9.gz</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">test_mr_rosetta.com</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">test_mr_rosetta.log</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Sorry: mr_rosetta failed...</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">********************************************************************************</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Sorry, a subprocess has failed...</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">END OF LOG FILE /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log :</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">SYMMETRY FROM INPUT SOLUTION: CRYST1 25.000 25.000 25.000 90.00 100.00 90.00 P 1 21 1</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Scoring the model /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/coord_mr.1.pdb</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Relaxing model at 3.0 A, generating and scoring 1 relaxed models</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Error message:</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">child process stderr output:</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"> command: 'sh /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh'</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh: line 3: 11915 Trace/BPT trap /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease @relax.flags > relax.log 2>&1</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Failed to run RELAX</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">******************* ERROR ENDING ***************</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Failed to run RELAX ...see log file in /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/relax.log</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">******************* ERROR ENDING ***************</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#000000"><br></font><font style="" color="#000000">The resulting log file showed the following:</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"> Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0"> Reason: image not found</font><br><br>phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following:<br><br><font style="" color="#0070c0">Running test_autobuild</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">FALED TO RUN: test_autobuild</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">**************************************************************</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Error: test_command_line_rosetta_quick_test failed</font><font style="" color="#0070c0"><br></font><br>After running the resulting test_autobuild.com script, the log file showed:<br><br><font style="" color="#0070c0">S_COORD_0001_ed_0005_ed.pdb</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">averaged_map_coeffs.mtz</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">coords1.pdb</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">fobs.mtz</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">relax.pkl</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">seq.dat</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">test_autobuild.com</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">test_autobuild.log</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Sorry: Failed to run autobuild</font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">ERROR MESSAGE: </font><font style="" color="#0070c0"><br></font><font style="" color="#0070c0">Sorry the file /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file)</font><br><br><br>The last error message was particularly confusing as that directory indeed does not exist on my machine, put was rather the directory path given as an example in the documentation.<br><br>I have two hunches for what could be going wrong, but I unsure how to fix either:<br><br>1. In the phenix documentation it says if using a mac, I might have to download some patches, but I could not find any on the Rosetta dowload page ;(.<br><br>2. The documentation also stipulates to specify a proxy server if behind a firewall using <br>export HTTP_PROXY=proxyout.mydomain.edu:8080<br>I am behind a firewall, but on my machine there is no proxy server listed under system prefernces-->advanced-->proxies. I can access my machine using a vpn, but don't know how to tell rosetta to do the same.<br><br>Thanks for all your help in advance and sorry that this is so long winded ;)<br><br>Cheers,<br><br>Joe<br><br></pre><br> </body>
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