mutate_residue not working

A MemoryError in Python is due to there not being a sufficient amount of memory on your system – it’s not a PyRosetta specific thing. As a general rule of thumb, you’ll want ~1 GB of memory for each instance of Rosetta you’re running (you can get away with less, depending on what you’re doing, but 1 GB is recommended to be on the safe side). This is not including any of the memory allocated for other things you’re running on your system. So if you were trying to run PyRosetta on an older system where you also had Word and your browser and Powerpoint and email client and Excel and PyMol and iTunes (and …) open, I’d recommend closing all of the programs you don’t immediately need and try running things again.

Hi Cheng,

Could you please try running ‘PyRosetta Self Tests’ from the start menu and see if all tests pass? (if you used installer this start-item should be created for you)

One of the test (test/Workshop6test.py in PyRosetta install location) is demo file which illustrate of how to use mutate_residue function. As Rocco mentioned it could be that your system just does not have enough memory (and by running build-in test i am trying to determent if that the case). You can also just run one test (Workshop6test.py) instead of whole test suite.

Thanks,

“cp” is the Unix & Mac way of copying files – it’s sometimes also recognized on Windows, depending on your settings. The error message just means that the PyRosetta Self Tests aren’t written to be maximally compatible with all Windows installations – it doesn’t necessarily imply anything about your problems. I believe you can substitute the “copy” command for “cp”, if you want to manually re-run the commands from the self-test.

The 1YY8.clean.pdb issue is due to current working directory issues. It’s trying to open test/data/workshops/1YY8.clean.pdb, but you’re already in the test/ directory, so things don’t work out. Do a “cd PyRosetta” in your terminal and then try “python testWorkshop6test.py” to see if that works better.