# [Chimera-users] Calculate distances between ligand atoms to select the most distant pair

Tom Goddard goddard at sonic.net
Fri Mar 4 10:35:36 PST 2016

```Hi Felipe,

If your aim is to get a measure of the size of the ligand you could use “measure inertia ligand”.  That shows an ellipsoid that matches the inertia of the atoms which is usually a decent approximation to the shape, and the radii along the 3 ellipse axes are reported in the Reply Log (in menu Favorites) as a, b, c.

open 2gbp
measure inertia ligand

Inertia axes for 2gbp 12 atoms
v1 =  0.710  0.376 -0.595   a =  4.106   r1 =  1.511
v2 = -0.671  0.106 -0.734   b =  3.321   r2 =  1.857
v3 = -0.213  0.921  0.328   c =  0.619   r3 =  2.362
center =   37.399   30.587    49.61

Longest axis is 2*a = 8.2 Angstroms.

If you really want the maximum pairwise distance then a simple Python script (attached) will do this.

open 2gbp
select ligand
open maxdist.py

Maximum distance between pairs of atoms among 12 atoms is 6.31 for #0:310.A at O6 and #0:310.A at O2

Tom

> On Mar 3, 2016, at 6:49 PM, Felipe Vasquez wrote:
>
> Hi,
>
> I am interested in select those two atoms more distant into a ligand. However, how could I estimate this so I have not to calculate the distance manually for all possible pairs one by one?
>
>
> Best regards,
>
>
> Andrés Felipe Vásquez J., BSc, MSc.
> Profesional - Grupo de Fisiología Molecular
> Subdirección de Investigación Científica y Tecnológica
> Dirección de Investigación en Salud Pública
> Instituto Nacional de Salud
> Avenida calle 26 No. 51-20 - Zona 6 CAN
> +57 (1) 2207700 ext. 1419
> Bogotá, D.C., Colombia
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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