[phenixbb] rosetta_mr autobuild failure

[Joseph Brock]

Hi all,

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

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:

1. phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up 

2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta 

3. phenix_regression.wizards.test_command_line_rosetta_quick_tests  

While the first was successful (ALL COMMAND_LINE TEST OK), the second reported the following error:

Error: test_command_line_rosetta failed

Upon subsequently running the test_mr_rosetta.com script created in the subdirectory, the following error was reported:

coords1.ali
coords1.pdb
fobs.mtz
mr_rosetta_quick.eff
perfect.mtz
seq.dat
test3.gz
test9.gz
test_mr_rosetta.com
test_mr_rosetta.log
Sorry: mr_rosetta failed...

********************************************************************************
Sorry, a subprocess has failed...

END OF LOG FILE /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log :

SYMMETRY FROM INPUT SOLUTION:  CRYST1   25.000   25.000   25.000  90.00 100.00  90.00 P 1 21 1

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
Relaxing model at   3.0 A, generating and scoring 1 relaxed models

Error message:

child process stderr output:
  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'
  /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
Failed to run RELAX


******************* ERROR ENDING ***************
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

******************* ERROR ENDING ***************


The resulting log file showed the following:

dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib
  Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease
  Reason: image not found

phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following:

Running test_autobuild
FALED TO RUN: test_autobuild
**************************************************************
Error: test_command_line_rosetta_quick_test failed

After running the resulting test_autobuild.com script, the log file showed:

S_COORD_0001_ed_0005_ed.pdb
averaged_map_coeffs.mtz
coords1.pdb
fobs.mtz
relax.pkl
seq.dat
test_autobuild.com
test_autobuild.log
Sorry: Failed to run autobuild
ERROR MESSAGE: 
Sorry the file /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file)


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.

I have two hunches for what could be going wrong, but I unsure how to fix either:

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 ;(.

2. The documentation also stipulates to specify a proxy server if behind a firewall using 
export HTTP_PROXY=proxyout.mydomain.edu:8080
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.

Thanks for all your help in advance and sorry that this is so long winded ;)

Cheers,

Joe


 		 	   		  
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