[Chimera-users] Assign distance between every atom and an axis or plane to an attribute

Oliver Clarke olibclarke at gmail.com
Wed Feb 24 05:21:38 PST 2016


I would like to iterate over all atoms in a model, measure the distance
between each atom and a predefined axis or plane in the session, and assign
the distance to an attribute associated with the atom. For bonus points I
would like to do the same for two models (the same protein in different
conformations), and then calculate the difference in this distance for
matched pairs of atoms.

The first part of this - iterating over every atom - I know how to do, more
or less, in the scripting interface (I am assuming there is no way to do
this kind of "iterate/run command/ assign command output to attribute"
operation in the attribute calculator).

But how do I measure the distance between an atom and a selected
plane/axis, and then assign it to an attribute that I can use for example
in Render by Attribute? I can see how to measure the distance between pairs
of atoms, but not between atoms and a plane or axis.

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