[Chimera-users] Capping a clipped sphere representation

Eric Pettersen pett at cgl.ucsf.edu
Sun Jun 26 17:56:20 PDT 2011

Hi Michelle,
	If you're willing to use an image that is just atom spheres, i.e. no  
surfaces, volumes, BILD objects, etc. then you can use the "conic"  


It will produce an image like the one I've attached.


	Eric Pettersen
	UCSF Computer Graphics Lab

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On Jun 24, 2011, at 6:50 PM, Elaine Meng wrote:

> Hi Michelle,
> Sorry, Chimera doesn't have capping of atomic representations or  
> ribbons. However, you can achieve something similar to the "sliced  
> spheres" by:
> (a) showing a molecular surface
> (b) clipping and capping that surface (capping occurs by default)
> (c) coloring the molecular surface to match the atoms (this occurs  
> by default)
> (d) the nonobvious step: coloring the cap to match the atoms too,  
> using Color Zone
> See the picture here to get some idea if this will meet your needs:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html 
> >
> It sounds like you figured out (a)-(c).  Then open Color Zone (under  
> Tools... Volume Data), select the protein atoms (for example,  
> command "sel protein"), click "Color" on the Color Zone tool to  
> color the MSMS surface (which includes the cap).  Radius values >2.5  
> should all be fine, the closest atom is used.
> However, at this point the coloring may look jagged. You could use a  
> finer triangulation of both the molecular surface and the surface  
> cap to make the former smoother, and get rid of jagged coloring  
> edges in both.
> There are several ways of increasing the vertex density of a  
> molecular surface, but the easiest to describe in email is this  
> command:
> setattr s density 5
> ... where the default density is 2.  You could try different  
> numbers, being aware that finer triangulations (higher density  
> values) use more memory and may make rotating the structure slower.
> To get a finer triangulation of the cap, start Surface Capping, for  
> example by clicking the "Surface capping..." button in the side  
> view, and increase the "Mesh subdivision factor," say to 3.
> Several of these steps are also covered in the "B-factor coloring"  
> image tutorial.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html 
> >
> I hope this helps,
> 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 Jun 24, 2011, at 4:12 PM, Michelle E. McCully wrote:
>> Hi,
>> I would like to create an image of a protein shown in van der Waals  
>> spheres with a clipped surface.  I'd like each individual sphere/ 
>> atom to be capped and colored the same color as the atom.  Is this  
>> possible?
>> I can show the protein in spheres and clip it using the side view  
>> dialog, but the clipped spheres show up as shells instead of solid  
>> balls.  I also have found directions for capping and coloring  
>> surfaces, but I don't see a way to make the clipped surface colored  
>> by atom.  It seems that building my protein out of sphere shapes  
>> and clipping that would give me the desired effect, but I was  
>> hoping there was something easier and built-in that I'm missing.
>> Thanks for your help,
>> Michelle
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