[Re-posting to the list because, as usual, I forgot to Reply All...]

Hi Greg - 

If I understand correctly (and just on a quick visual inspection in PyMOL it looks like I'm at least close), the sphere_scale setting will scale the size of the sphere relative to the van der Waals radius of the atom.  So at sphere_scale == 1, Carbon will be ~1.70, Oxygen will be ~1.52, Nitrogen ~1.55, and so forth.  To have a CA atom of 3 radius, you would use sphere_scale of ( 3.0 / 1.7 ) = 1.76.

Hope that helps,


Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016

On Jul 26, 2013, at 3:23 PM, Gregory Ryslik <rsaber@comcast.net> wrote:


I'm a fairly new user to PyMol and am having some trouble with the sphere_scale command. I understand that if I want to draw a sphere around the x'th ca atom, I can use:

show spheres, ////X/ca

However, what if I want that sphere to have a radius of 3 angstroms, or 6 angstroms, etc.

 I understand I can use set sphere_scale, 1, ///X/ca but what is the default scale of 1? Is it 1A, is it something else?

Thank you for your help!

Kind regards,
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