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I would like to measure the distance between two active sites in a protein complex (pdb), but I do not find a straightforward way to do it.

To be more precise I need the distance along the surface of the protein and not the linear distance that would go through the protein, and which the distance wizard will give.

I have access to Pymol and would prefer a solution using that software although I would consider other as well. Thanks.

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  • $\begingroup$ What "surface" you prefer? $\endgroup$ – Mithoron Jul 6 '17 at 17:54
  • $\begingroup$ Solvent accessible surface $\endgroup$ – user46680 Jul 6 '17 at 17:55
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I would use linear distances between a suitable amount of fixed points as an approximation. You cannot measure exact distances along a rough surface, as the distance will vary depending on minimum measuring size. This is known as the coastline length paradox in math. https://en.wikipedia.org/wiki/Coastline_paradox

In theory the length would approach infinity as the measuring size approaches 0.

In practice you can get around the issue if you use a step size compatible with the smallest stable feature.

A suitable measuring size would probaly be in the order of ~10^-11 meters. (1/10 the size of an carbon atom).

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