How to upgrade a web service to ASP.NET 4.0 with out affecting other services

After you have installed .NET 4.0 on the server open a command window and run:

C:\WINDOWS\Microsoft.NET\Framework\v4.0.30319\aspnet_regiis.exe -norestart -s W3SVC/ID/root/

Replace ID in the line above with the Identifier of the Web Service.  The Identifier can be found by starting the IIS snap in and clicking on the "Web Sites" folder and looking in the right pane.  

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