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I have a service with three layers that I publish to our Enterprise 10.6.1, from ArcMap 10.6.1. I know that when I publish the service from my MXD, I can check/uncheck the box in the Mapping Capabilities window. But this will turn it off for all layers, correct? I would like to turn it off for one layer and leave it on for the other two in the service. Am I able to do that, either at the MXD level or at the Portal Manager/ArcGIS Server Administrator Directory level? enter image description here

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As far as I am concern this is not possible. The operations are referring to the full map service and not to the "sub-layers". As it says in the documentation:

Selecting this option allows client applications to query the features in your map service. ArcGIS Server Docs

Why don't you split the layers into different services?

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    From a service management standpoint, I'd rather keep everything together and organized, without splitting up anything. If it's not possible, no big deal. Thanks for your input. – Dave Sep 17 '18 at 12:45

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