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Article ID: 1595 - Last Modified: August 22, 2013

Find Homolog and Secondary Structure Prediction in Prime do not work. I do not have a local installation of the BLAST sequence database, so I was expecting these steps to access the NCBI site remotely. How can I fix this problem?

Starting with Suite 2011, the standard installation provides the necessary components to search for homologs/templates and to run secondary structure prediction by remotely accessing the NCBI (BLAST) site.

From Suite 2012, there is no difference in the installation between web-based searching and local searching.

In Suite 2011, it's possible that the necessary components were accidentally removed or corrupted. To reinstall them, download the following file.

For Windows:

ftp://ftp.schrodinger.com/support/hidden/prime/Suite2011_webbased/Windows/Schrodinger_webBLAST_Windows.zip

For Linux:

ftp://ftp.schrodinger.com/support/hidden/prime/Suite2011_webbased/Linux/Schrodinger_webBLAST_Linux.tar

On Windows, unzip the file and choose as the destination folder the location of your Schrodinger installation (typically, C:\Schrodinger2011). On Linux, untar the file, cd into the Schrodinger_webBlast_Linux directory, and type ./INSTALL in a shell.

If you are using a proxy server for access to the web, you may have to set up access to run a BLAST search on the web.

Related Articles:

#1014: I cannot get a PsiPred secondary structure prediction in the Edit Alignment step even though I have installed PsiPred...
#816: I chose to do web-based homology searching with Prime, and can find homologs for my query, but I get an error when tr...

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