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How to set up external C++ folding server

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How to set up external C++ folding server

For many of the  Rosetta applications, I am required to connect to an external server to process my requests and handle the modeling and structure predictions.  How exactly am I  supposed to do this?  Is there a detailed tutorial on how to do this?  Or is it because I did not install PyRosetta correctly?  I am doing comparatve modeling/structure prediction.

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Sat, 2016-06-11 10:54

For homology modeling, the part of the process that is purely Rosetta and would be in PyRosetta comes as the last part of the process.  Secondary structure prediction (sparksx, hhpred), template threading (tmalign), etc, are external programs.  They don't belong to Rosetta, so they won't come with PyRosetta.  If these are the "external servers" to which you refer, you aren't doing anything wrong, it's just a cost of doing business.

This particular problem is largely restricted to homology modeling.  Most protocols (docking, design, etc) live entirely inside Rosetta.

Let me know which peices are giving you trouble and I can clarify further.

Sat, 2016-06-11 14:51

Thank you for your response.  Just to clarify, some of the protocols listed in Interactive Rosetta do not run inside of Rosetta? Do you have any reccomendations that would help me set up Interactive Rosetta to connect with these external programs like sparksx and hhpred?  I saw a youtube video where this is accomplished.  The link is  Sorry, I'm really new to this and I would appreciate all of the help I can get.

Sun, 2016-06-12 09:27

Unfortunately I don't know anything about this particular tool beyond what I saw at RosettaCON last year.  I'll ping the author to see if they can help further.

Sun, 2016-06-12 10:20

I guess I should note that homology modeling is not something one does on a laptop - you should be thinking in the mid-hundreds of CPU hours for the problem.  (I mean, you can run one model less, but Monte Carlo sampling demands repeats).  That may be the source of the confusion?

Sun, 2016-06-12 11:11

I understand that the homology modeling does not run locally on my computer.  I was just asking if the homology modeling came with Rosetta, or if I had to somehow connect it to an external program (like the ones that you mentioned).  On the Interactive Rosetta menu, it lists homology/comparative modeling as one of the options, but when I attempt to use it, it gives me an error message saying that I need to connect to an external server.  I believe that the external server is  supposed to handle the actual math and modeling, as mentioned in the video.  I've been trying to figure out how to exactly do that.

Mon, 2016-06-13 17:24

Hello seanle24245, I can provide you with the notes that I took when I set up a small Linux Rosetta cluster in the laboratory I used to be in.  Unfortunately I am no longer in academia and do not have access to Rosetta anymore, so I probably won't be able to help much beyond providing these notes.  You will need to have at least a couple of computers that are available to run as backend computing machines.  Like smlewis indicated, you'll need many CPU hours to perform homology modeling in Rosetta whether or not you use InteractiveROSETTA or just regular Rosetta at the command line.  I uploaded two files: one detailing how to set up various modules for InteractiveROSETTA and one with general instructions on how to set up the backend machines.  For InteractiveROSETTA setup, you will need to follow the instructions listed under "TO SETUP THE LINUX INTERACTIVEROSETTA SERVER" and "INSTALLING THE FRAGMENT-GENERATION DEPENDENCIES."  Installing the fragment generation dependencies is absolutely needed for homology modeling whether or not you use InteractiveROSETTA.  The backend machine setup was mostly specific to our particular hardware setup, so you probably will not be able to follow it verbatim but it should give you a good idea of all the steps involved in setting up a machine.  If you are not comfortable with troubleshooting this sort of thing, you may want to enlist help from someone who is comfortable with IT.  Most of it is not terribly complex, so it can be set up as long as the person setting it up has familiarity with Linux/networking and can troubleshoot.

Tue, 2016-06-14 16:54

Hi there!  My name is Benjamin and I'm currently in charge of development for InteractiveROSETTA.  I'm actually currently working on making the setup of a server for InteractiveROSETTA easier and more understandable.  There are still some bugs to be worked out, but I can help you get a server setup.  Do you have a linux cluster or something like that that you want to use as an external server?  Or were you asking if there were pre-existing servers to connect to?

Thu, 2016-06-16 07:51

Hi Benjamin,

I am looking for a pre-existing server to connect to.  Thank you for your assistance.


Sun, 2016-06-19 18:30