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

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 24 09:18:58 PST 2016

Hi Oli,
If the object (centroid, axis, or plane) was created with Axes/Planes/Centroids or the “define” command, you can specify it by identifier in the “distance” command, for example:

distance c1 c2
- measure the distance between centroid c1 and centroid c2
distance signed p2 :313.a at o
- measure the signed distance between plane p2 and atom O in residue 313 of chain A


I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 24, 2016, at 5:21 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi,
> 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.
> Cheers,
> Oli
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