Shipbucket

A very nice looking ship- one that could perform 'station ship' and 'colonial cruiser' duties after Final Victory.
A very flexible vessel.

It does look like a huge colonial sloop doesn't it?

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Looks like one, has the necessary equipment, provides the necessary facilities... would work perfectly.

Yes, the Mutzenbachers were very versitle ships. The 'Peter Beutler' was refitted as oceanic research vessel in 1952 and came as 'Sternenschweif' to the oceanographic institute. Most of the armament and directing equipment was removed and small labs installed. The aft deck no carries a flight deck with two Weserflug-VTOLs. Just a 5,5cm-twin and a 5" twin DP are still on the fore deck. Finally the 'Sternenschweif is just a loan by Kriegsmarine to the institute until they get their very own vessels.

The painting is not the usual 1946 invasion camo, it is nearly as real german research vessels are painted.

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The 'Rainer Merkant' was given to the new formed independent state Südwestafrika as gift. The catapult was removed and a triple 'Geier'-launcher installed. Ammo was stored behind the funnel. When given away the now named 'Grootfontein' was still in blueish camo.

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As far as research ships go, it's hard to imagine a period warship being much use without a new-construction deckhouse for labs, equipment, etc.

...or any conceivable reason why it would have armaments.

There is much space from former ammo stores und below the flight deck. The ship was given to the institute under the rule it could go back into active service any time. So the fore arms were kept. And who knows what heavy armed monsters are lurking at the unknown areas of the world? Better safe than sorry.

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In this case it'll be sorry, since she won't be able to seek port anywhere since, like you said, she's operated by civilians yet she carries weapons. Surprisingly, most governments tends to take a dim view on that sort of thing.
Also, why retain the floatplane if you're going to have VTOL aircraft? (Unless of course the civilian engineers realize just how mechanically unsound the Weserflug design was)

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Source Materiel is always welcome.

Some 'civilian' Sealift Command vessels are armed; the Mars class combat stores ships had as many as six 3" guns mounted at one time or another.
And if one really desires to get technical- ALL U.S. Coast Guard ships were owned by the Department of the Treasury or the Department of Transportation until 2002. This means that they were not military vessels at all, but armed civilian law enforcement vessels- occasionally rather heavily armed ones at that!

I see little real difference here- if the vessel's operational crew was taken for the Reich's 'Coast Guard Equivalent,' then it could probably get away with being armed while still being 'civilian' in nature.