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I can establish a connection to my university VPN (Cisco IPSec). In addition I have to set a proxy, in this case I have the URL of a .pac file.
When I set this in the VPN-settings, the proxy is not used by Safari or Chrome. How can I set proxy settings for my VPN? I don't want to put this in the main network settings because I only need the proxy for VPN.
Setting it in the VPN connection settings works as expected for me.
Make sure you check the Web Proxy (HTTP) checkbox (or other types of proxies if required) and fill out the correct proxy server details. You probably also need to enable "Send all traffic over VPN connection" in the VPN's advanced configuration.
Afterwards, make sure you apply the settings by clicking on the Apply button.
Alternatively, you can set up different network locations. You can add a location in the Network preference pane and configure different values for the proxies and other settings on the main network interface. You will have to manually select the appropriate location for switching settings though.
Under Mavericks this should work fine. Once you have all the security details set in your VPN connection click on Advanced and then Proxies.
Make sure you select Automatic Proxy Configuration and put the complete URL provided by your IT staff into the URL field. This will almost certainly be different to the proxy config file used by a computer that lives inside your network.
You don't want to send all traffic over the VPN. Now a web site internal to your network will use the proxy but those outside will not. This is the behaviour you want.
It may be useful to actually look at the .pac file. You can do that by entering the URL into the address field of your browser and it should be loaded as a text file.
The only case where you want all traffic to go over the VPN is if you are accessing an external web service that your organisation pays for that authenticates through the network - this is usually things offered by the library such as law services or special dictionaries.
