I'm looking at the graphics, and my protein looks very VERY similar to the native version. However, it's rotated significantly around two different axes, and the RMSD is over 7!

Is there some reason that the orientation of the molecule is important? It doesn't look like either of the ends is tied down, and even if it were, it seems like it shouldn't matter.

To make it clearer, if the native structure were rotated 180 degrees around the y axis, wouldn't it still have the same low energy?

Of course it's entirely possible that I'm misunderstanding the picture -- the 3D on the screen is less than perfectly clear. I'm just wondering (or making sure) whether there's a reason that orientation should matter.

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I'm looking at the graphics, and my protein looks very VERY similar to the native version. However, it's rotated significantly around two different axes, and the RMSD is over 7!

Is there some reason that the orientation of the molecule is important? It doesn't look like either of the ends is tied down, and even if it were, it seems like it shouldn't matter.

To make it clearer, if the native structure were rotated 180 degrees around the y axis, wouldn't it still have the same low energy?

Of course it's entirely possible that I'm misunderstanding the picture -- the 3D on the screen is less than perfectly clear. I'm just wondering (or making sure) whether there's a reason that orientation should matter.

RMSD is after "optimal superimposition," so orientation does not matter. It is likely that what you are seeing is an illusion due to the limitations of the visualization, as you suggested.

...RMSD is after "optimal superimposition," so orientation does not matter. It is likely that what you are seeing is an illusion due to the limitations of the visualization, as you suggested.

So it's OK to stand my computer on its side then?


;-)