Say I have a protein structure consisting of multiple alpha-helices. How do I select one alpha-helix and position the entire protein so that this one alpha helix is perfectly vertical, or horizontal?
To my knowledge this probably isn't really possible, though you may have more luck asking over on the chimera users forum/mailing list. If it is, I suspect it's going to be difficult.
The only possible approach that springs to mind might be to define a centroid axis through the helix, but I still don't know if its possible to position the axis relative to the x,y,z planes.
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