Aha! I knew there was a better way of doing this, but I was stuck on a machine that only had an old version of PyMOL. Assuming you're using PyMOL 1.0 or newer, you can just use pseudoatom. To create a sphere of radius 10.0 at the xyz position (50.0,60.0,12.0), just do this:

pseudoatom mysphere, pos=[50.0,60.0,12.0], vdw=[10.0]

it will appear as a kind of cross at first. to show it as a sphere, type

show spheres, mysphere

to make it partially transparent, type

set sphere_transparency, 0.5, mysphere

The sphere that you get will look kind of blocky. You can get a perfect sphere by raytracing, e.g. typing


If you don't mind the fact that it won't be transparent, you can get a perfect sphere in the normal viewer by typing

set sphere_mode, 5

To go back to normal spheres after you've done that, type

unset sphere_mode

I think this will be easier than the other way I recommended.



On Tue, Jul 7, 2009 at 1:55 PM, Benjamin Michael Owen <owen13@marshall.edu> wrote:

I'm trying to use a suggestion another pymol user sent to create a sphere of a specific size in a pdb file. Is this the correct coding? I have no experience doing any kind of programming so I am not sure if I did this right. I put the text I entered in in red if that helps anything.


create sphere, resi 24 and resi 864 create a new object from resi 864

alter sphere, vdw=10.0 # 28.5

rebuild # necessary if spheres have already been shown

show spheres, sphere

alter_state 1, sphere, x,y,z = 50,60,10 # set desired x,y,z coords

set sphere_transparency, 0.5, sphere # make it transparent



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