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How to get Steam version of Indy4 work with ScummVM and Dosbox
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ScummVM modifications are not needed. Game works like original.

ATLANTIS.000 is missing from Steam version. It is inside the
"Indiana Jones and the Fate of Atlantis.exe".

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Buy and install Indiana Jones and the Fate of Atlantis from Steam
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Please buy the game. It is not so expensive. Price is Only $4. 
Wine for downloading worked great.

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Make backup
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Accidents happens.

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Use dd
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command: "dd if=Indiana\ Jones\ and\ the\ Fate\ of\ Atlantis.exe of=ATLANTIS.000 bs=1 skip=224336 count=12035"

Just copy/move ATLANTIS.000 to the same directory with ATLANTIS.001.

bs, tells how many bytes is one block. 
skip, tells how many blocks are skipped from the start
count, tells number of blocks to be writen

Finding right parameters to dd were a lot of easier than for the Indy3. I have Amiga version where I checked
startpoint.

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Result
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* No need to modify ScummVM
* Dosbox compability
* Windows/Wine free gameplay