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RosettaCommons / PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
https://rosettacommons.github.io/PyRosetta.notebooks/
MIT License
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Light chain gene identity required in Notebook 12.02 #57

Closed OLaprevote closed 3 years ago

OLaprevote commented 3 years ago

In the third antibody design notebook, the AntibodyDesignMover rabd2 crashes when applied, giving the error message:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-7-2dc5bb52b04a> in <module>
     10 rabd2.set_light_chain("kappa")
     11 if not os.getenv("DEBUG"):
---> 12     rabd2.apply(pose)

RuntimeError: 

File: /home/benchmark/rosetta/source/src/protocols/antibody/database/AntibodyDatabaseManager.cc:367
[ ERROR ] UtilityExitException
ERROR: Antibody Design requires the identity of the light chain gene. Please set it using the -light_chain option.  PyIgClassify can be used to determine the light chain gene.

XmlObjects calling the AntibodyDesignMover work fine, only the python AntibodyDesignMover seems to crash. Looking up PyIgClassify in pyrosetta API reference doesn't give any result. Setting -light_chain kappa during pyrosetta.init fixes this, so I fear the problem comes from PyRosetta.

Using PyRosetta version 2020.39+release.9ee477a. The required version is 2020.38 in environment.yml, so it would be worth checking with this one and a more recent PyRosetta release.

jadolfbr commented 3 years ago

Thanks for reporting this! Fixed in PR #61

jadolfbr commented 3 years ago

This will actually be fixed via C++ code in a Rosetta merge today.