RosettaModel blueprint for PyRosetta

[Anonymous]

Hello everyone,

I started learning PyRosetta in December 2014 using the newest workshops currently available and a number of other online resources. I would like to learn how to design protein scaffolds and enzymes de novo, and to that end I am currently trying to see if I can achieve a specific small protein topology using pre-defined secondary structure characteristics, similar to the strategy used in the Kuhlman et al. 2003 paper on the design of Top7. I am trying to make use of the RosettaModel blueprint to set the lengths of each secondary structure component and other hydrogen bonding constraints, but I cannot find documentation on how to use the blueprint in PyRosetta through Ipython. I tried out the pyrosetta toolkit as well, but it does not seem as though blueprints can currently be created via the GUI. Any recommendations are appreciated!

Thanks a lot for your help,
Ben

[Anonymous]

Hi Ben!

I believe that components of RosettaRemodel can be run through PyRosetta, but it will take some exploring to use it. We don’t yet have API documentation on some of the newer Rosetta modules (EnzDes, RosettaRemodel, RosettaAntibody, etc.). We are currently discussing this as a community and hopefully, sometime in the next year, the documentation page that holds all the docs and RS docs should hold extended PyRosetta APIs as well. Part of it is figuring out how to use it ourselves.

That said, you will need to look into the protocols/forge/remodel namespace. The main C++ app calls protocols/forge/remodel/RemodelMover as the workhorse., pretty much exclusively – so ideally, you should be able to run the full Remodel through the RemodelMover. Not sure its ever been tested though. You can then also take a look at this file in C++ to see how it works with the other remodel classes (BlueprintBDR, etc, etc.)

As for the GUI, yes, I don’t currently have a window to make a blueprint file or run remodel. I can definitely think about adding it at some point in the future. I started a C++ GUI for remodel file creation, but it didn’t really get anywhere. Perhaps I could resurrect that. The one thing you can do is output a basic blueprint file for use in redesigns – File -> Export -> Basic Blueprint File (after loading a pose).

Good luck! I can try to look more into how the blueprint code works over the next week or so if you run into some problems.

-Jared

[Anonymous]

I know this is an old post, but I stumbled across it searching for something else and I thought I’d brazenly (yet secretly very embarrased) add a link to a blog post of mine about using Remodel in PyRosetta (in Jupyter, not GUI). It includes details on a Python module to make blueprint files.

 

[Anonymous]

Hi Jared,

Thanks a lot for the quick and detailed response. I will look into the remodel namespace, as you suggested. If I am able to get the RemodelMover running easily through PyRosetta I will post the updates to this thread, but for now I am going to mark it as solved because you answered my question really thoroughly and gave me some great tips. I really appreciate it.

Thanks again,
Ben

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