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Click on the ellipses corresponding to context menu icon of the newly imported Server Certificate and select Apply

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Select the correct SSO Server from the drop down...

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Hit Apply

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Certificate 

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Select Apply To

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Select the type of service to which the certificate will be applied, e.g. SSO Server

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Select the type of certificate, e.g. Web SSO Certificate

Select the instance(s) the SSO server(s)

Click Apply

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