[Chimera-users] Capping a clipped sphere representation

[Eric Pettersen]

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"  
command:

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/conic.html

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

--Eric

	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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