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Normal Sphere Representation Example


To enable the spheres representation do the following for any selection SEL,

show spheres, SEL

Adjusting Sphere Size

alter selection, vdw=number


Shrink the size of all Iron atoms:

alter elem fe, vdw=1.0

Dramatically enlarge all spheres in an object

alter object, vdw=4.0

OpenGL Shaders & Spheres

Newer OpenGL supported cards (like the NVidia 5950 Ultra, or the 6800 GT Ultra) support Shaders. Shaders are best used for massive numbers of molecules that are to be represented as spheres. Typical ranges will now include 500 000 to 3 000 000 atoms! Take a look, the following example is of a viral nucleocapsid: 261 240 atoms! Performance and visual quality -- without rendering -- are far improved.

Comparing Shaders and No-Shaders

Normal spheres: no shaders
(sphere_mode=5) Shader Spheres

To turn on Sphere Shaders use

set sphere_mode, 5
as spheres, SEL

where SEL is the name of your selection. Getting normal sphere mode back is easy:

set sphere_mode, 4
as spheres, SEL

Enabling Shaders

If the above doesn't work, then you may need to rebuild PyMol so that it builds the shaders source code. To do this, you simply need to edit the setup.py file before you build PyMol.

Find the appropriate line in your setup.py file depending on your system. The relevant lines are, first for Windows,

if sys.platform=='win32':

and for Windows using Cygwin

elif sys.platform=='cygwin':

and finally for *nix or other systems as the following


Under this code, find the

#           ("_PYMOL_NUMPY",None),

and make it

#             ("_PYMOL_NUMPY",None),

I just added the



See the Installation Page to find out how to build PyMol.