Calculate distances between ligand atoms to select the most distant pair
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
Hi, Not sure I exactly understand the question, but I’ll try to answer anyway. If you use command “measure distance” with two sets of atoms it will report the minimum of all the pairwise distances. However, I don’t know of any way to get the maximum of all the pairwise distances other than doing all the pairwise measurements individually. Everything can be done with a python script, but somebody else would have to advise on that. Example for getting minimum distance between ligand and residue 255 of pdb 2gbp, commands: open 2gbp measure distance ligand :255 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 3, 2016, at 6:49 PM, Felipe Vasquez <anfelvas@gmail.com> 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. Be
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
participants (3)
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Elaine Meng -
Felipe Vasquez -
Tom Goddard