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 setup_RosettaCM.py. 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 setup_RosettaCM.py --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 "setup_RosettaCM.py", 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
The setup_RosettaCM.py 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 setup_RosettaCM.py --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.)
thanks, the --rosetta_bin worked.