Re: [PyMOL] sphere_scale help

[Sampson, J. <Jar...@ny...>]

[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 ~1.70Å, Oxygen will be ~1.52Å, Nitrogen ~1.55Å, and so forth.  To have a CA atom of 3Å radius, you would use sphere_scale of ( 3.0 / 1.7 ) = 1.76.

Hope that helps,

Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/




On Jul 26, 2013, at 3:23 PM, Gregory Ryslik <rs...@co...<mailto:rs...@co...>> wrote:

Hi,

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,
Greg
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