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I'm having trouble with two maps, both UTM33N/WGS84. They should be exactly on top of each other but there is a slight shift between them of probably a few hundred meters or so. enter image description here

I Tried to adjust this with the Vector Affine Transformation Plugin but didn't succeed. I don't know how to use it.

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Have a look at the answer here - qgsAffine is not easy to use, but works once you know the numbers to plug in. I do agree with @Darren Cope's suggestion though - check the origins and intended scale of each layer to see if they even should line up. – Simbamangu May 10 '12 at 16:50
Are you sure both datasets are on wgs84? A few hundred meters could be due to different datums. – mkennedy May 10 '12 at 18:08
up vote 3 down vote accepted

I think we are getting somewhere. The original shapefile (contained in appears to be Pulkovo 1942(83)/Gauss-Kruger Zone 4, which is EPSG:2398. So if you load this into QGIS and set its CRS to EPSG:2398, then save it as EPSG:32633 this should do the trick. Nick.

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Strange. Now it woked! Thanks! – desputin May 12 '12 at 6:30

To me this looks like a 'scale' issue. The layers appear to be drawn at a different level of detail, and thus will never line up exactly. Am I missing something?

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The curves look to have the same level of detail to me. – nmpeterson May 10 '12 at 17:40
@nmpeterson; I really don't think so. Look in the bottom-left corner specifically. There's no way this is can be a 'matching' dataset. Please don't downvote without closer inspection! – Darren Cope May 10 '12 at 18:33
I inspected rather closely. The blobby features' coastal path seem to be a convex hull of the underlying polygons, but shifted dramatically (as the OP believes). – nmpeterson May 10 '12 at 18:44
It doesn't help that the underlying features seem to be only a sample of a larger dataset, making it more difficult for us to know where the actual "coastline" is in certain places, like the lower left -- are those actually islands, or just polygons whose neighbors aren't a part of the sample? – nmpeterson May 10 '12 at 18:46
Which is the dataset with the problems? If it's not confidential could you post a download link? Nick. – nhopton May 10 '12 at 19:31

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