# PSIPRED secondary structure prediction in PyRosetta

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PSIPRED secondary structure prediction in PyRosetta
#1

Dear All,

I am trying to preform PSIPRED secondary structure prediction in PyRosetta. This is my code so far:

psipred = pyrosetta.rosetta.core.io.external.PsiPredInterface(' ') #<--- What goes here?
psipred.run_psipred(pose , 'blueprint') #<--- Is this correct?

I think I am close at getting it to work, but I am not there yet; what goes in the first line? (pydoc3 says the argument in the first line should be cmd: str and I don't know what that is)

Is the second line correct? are there any other methods I should include to preform a correct PSIPRED secondary structure prediction for Abinitio?

I have attached the blueprint file that I think is required.

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Fri, 2017-09-01 22:56
ac.research

Rosetta doesn't actually have the PsiPred secondary structure alignment algorithm internally. The object you're using is actually intended to be able to invoke an external program which will run PsiPred. The argument to the constructor is actually the command line which will run the PsiPred algorithm on your computer. What Rosetta does is effectively generate a temporary fasta file from the pose, add that temporary filename to the end of the command you've passed, and then ask your shell to run that commandline. It then looks for the expected outputs and then parses them.

So in order to use the PsiPredInterface object, you would need to have the appropriate version of PsiPred already installed on your machine, and working from the commandline interface (external to Rosetta).

The second argument to run_psipred is the blueprint string -- basically a string of the same length as the pose, with 'H'/'E'/'L' for the desired secondary structures. The PsiPredInterface was intended to be used "on-the-fly" during design calculations using the RosettaRemodel protocol, and as such isn't really set up for a more general running of PsiPred for things like fragment picking.

For generating the input files for fragment picking - particularly as you're using PyRosetta - I'd recommend just running the psipred executable directly.

Mon, 2017-09-04 09:52
rmoretti