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I am trying to move beyond the tutorials to make homology models for my own proteins. We have just recently installed Rosetta and I'm still running into a lot of basic errors where the scripts cant find parts of the software package due to path errors.  Can someone explain how to fix this one in the  Or at least how to get started on debugging?  Most of the compiled applications in /rosetta/main/source/bin/ do work for me.  I suspect hard coded path errors or non-existant logical names in the python code, but again, how do I debug?

[smbrow3@vnode170 MCR]$ python --fasta ANME2_HR1.fasta --alignment_format clustalw --alignment mcrG_4.aln --templates 1E6V_3.pdb,1E6Y_3.pdb,7NKG_3.pdb  --verbose
Using rosetta from /users/smbrow3/Rosetta/main/source/bin
Traceback (most recent call last):
  File "", line 558, in <module>
    assert(os.path.exists(rosetta_bin)), "%s doesn't exist"%rosetta_bin
AssertionError: /users/smbrow3/Rosetta/main/source/bin doesn't exist

Post Situation: 
Mon, 2021-06-28 07:13

The script by default looks for Rosetta within the ~/Rosetta/main/source/bin directory. This can be changed with the --rosetta_bin option of that script. So you should be able to do something like `python --fasta ANME2_HR1.fasta --alignment_format clustalw --alignment mcrG_4.aln --templates 1E6V_3.pdb,1E6Y_3.pdb,7NKG_3.pdb  --verbose --rosetta_bin /rosetta/main/source/bin/` and have it find the proper directory.


By the way, most Python scripts with Rosetta will respect the `--help` or `-h` option, and will print out some help text where the availible options will be documented. (Though will various degrees of intelligibility -- "rosetta path" is probably not that forthcoming.)


Mon, 2021-06-28 07:44

thanks, the --rosetta_bin worked.

Tue, 2021-06-29 11:41