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Mathematica should render the secondary structure in the usual way when you import pdb files. I dont know why this doesn't work with the example you provided. I thought there might be a size limit for the protein but I managed to import much bigger proteins such as 1YHU and they got rendered without problems... strange. ...


1

The problem is that your data is sorted in such a way that ListSurfacePlot3D can't draw the surfaces correctly. You can fix it by scrambling the data: ListSurfacePlot3D[RandomSample[xyz, 100000], BoxRatios -> {1, 1, 1}] However, this gets very slow with the increasing number of points and I'm assuming it won't be able to draw the elevation changes to ...



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