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Is it possible for me to programmatically create in linux centos 6.4 or a windows with only arcGIS Engine runtime (single use license without sdk)?

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Did you try IMapDocument.Save in the java sdk? –  Kirk Kuykendall Aug 12 '13 at 21:57

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Not having the SDK is a major wrench in the gears here. If you have an MXD already on disk, you could use arcpy.mapping.AddLayer in a Python script on a MapDocument object and use MapDocument.saveACopy to save out. You can run ArcGIS' Python from an Engine install.

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Thanks, turns our i had two python installs (one from arcgis 10.1 and one from arcgis 10.0) and my IDE was using the wrong install for my runtime license, ands thats why arcpy import was failing –  Moggy Aug 13 '13 at 14:46

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