# setup_RosettaCM.py

3 posts / 0 new
setup_RosettaCM.py
#1

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

Post Situation:
Mon, 2021-06-28 07:13
browns02

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.)

Mon, 2021-06-28 07:44
rmoretti

thanks, the --rosetta_bin worked.

Tue, 2021-06-29 11:41
browns02