Article ID: 1595 - Last Modified: April 30, 2012
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.
In 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.
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.
Keywords: Prime, BLAST, find homolog fails, secondary structure prediction fails
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