I cannot get a PsiPred secondary structure prediction in the Edit Alignment step even though I have installed PsiPred on my system. What is the problem?

In Suite 2010, in order to run Prime structure prediction, even if you use web-based searching, there are still some components that will have to be installed in order to run the PsiPred secondary structure prediction. (This is not the case from Suite 2011 on.) If you are using the web-based search, you will have to download and install the third-party software and databases available here:

ftp://ftp.schrodinger.com/support/hidden/prime/Suite2010_webbased/Linux/

If you have an independent installation of PsiPred, you will have to set an environment variable so that Prime can locate it. See the Installation Guide for details.

Note that PsiPred is not available on Windows.

Keywords: Prime, SSP, PsiPred, structure prediction, Blast, secondary structure prediction

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