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 Reply Log shows Maximum distance between pairs of atoms among 12 atoms is 6.31 for #0:310.A@O6 and #0:310.A@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?
Thanks in advance for your help.
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@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users