setup_RosettaCM.py

[Anonymous]

 

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

 

[Anonymous]

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.)

 

[Anonymous]

thanks, the –rosetta_bin worked.

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