Hi Aaron,

Are you running rosetta.build_phenix_interface in a shell with administrative privileges (i.e. "sudo -i")? Because Phenix is in /Applications and Rosetta is in /usr/local, the command needs administrative privileges to write in those directories.

Also, I am current testing newer versions of Rosetta since Rosetta 3.9 seems to have some problems on macOS. I'll update this thread and the documentation once we've settled on a version.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909


On Tue, Aug 21, 2018 at 1:45 AM Aaron Oakley <aarono@uow.edu.au> wrote:
I have repeatedly tried to install Rosetta for use in Phenix with zero success.

System: macOS 10.13.6
Phenix version: phenix-1.14rc1-3177
Rosetta version: 3.9 (rosetta_src_2018.09.60072_bundle)

Relevant environmental variables:

ROSETTA3_DB=/usr/local/rosetta_src_2018.09.60072_bundle/main/database
ROSETTA_TOOLS=/usr/local/rosetta_src_2018.09.60072_bundle/tools
ROSETTA3=/usr/local/rosetta_src_2018.09.60072_bundle/main/source
PHENIX=/Applications/phenix-1.14rc1-3177
PHENIX_VERSION=1.14rc1-3177
PHENIX_ROSETTA_PATH=/usr/local/rosetta_src_2018.09.60072_bundle

rosetta.build_phenix_interface —seemed— to work OK.
However...
rosetta.run_tests fails with

DEBUG dumping error message
ERROR: Rosetta exited with status 1
stderr output:
BACKTRACE:
0   libcore.3.dylib                     0x0000000114b0e4e6 print_backtrace(char const*) + 54

…40 lines of traceback crap…

Traceback (most recent call last):
  File "/Applications/phenix-1.14rc1-3177/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module>
    run(sys.argv[1:], create_dir=True)
  File "/Applications/phenix-1.14rc1-3177/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run
    debug=params.output.debug)
  File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__
    self.run_jobs()
  File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs
    check_result(result)
  File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result
    raise RuntimeError("Aborted due to error in job %d." % result.job_id)
RuntimeError: Aborted due to error in job 1.


Any ideas?

Aaron Oakley
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org