[Chimera-users] center of the molecule

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 10 14:09:43 PDT 2009

Hi Dave,
The reason the spheres look solid is that "surface capping" is turned  
on by default.  You can just turn off surface capping so that they  
will look like thin shells when clipped.  There are a bunch of ways to  
show the capping dialog, but one easy way is to click "Cap clipped  
surfaces" on the Side View.  In the dialog, just uncheck "Cap surfaces  
at clip planes".   I don't think we have any command to do that, or  
any preference for capping to be turned off, sorry.

Formerly capping was off by default, which is why the button says "Cap  
clipped surfaces" instead of "Uncap" or "Control surface capping"  
which would be more descriptive of the current situation.

The things created with the "shape" command are surface models, and  
you can select them, show them as mesh, change their colors, make them  
transparent, etc. using the Actions... Surface menu or the Selection  

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 10, 2009, at 1:58 PM, David Chenoweth wrote:

> Hi Elaine,
> I need to do something very similar to the procedure that you sent  
> to Bala for placing a sphere at a designated location except I need  
> to place shells of concentric spheres at a point in space. I can use  
> the command below to place multiple spheres at a point but the  
> spheres are filled with the color. I would like to have just a thin  
> shell or the surface of multiple spheres placed at a point that  
> increment in their radius by 1 angstrom intervals. I would then like  
> to make the spheres slightly transparent so I can overlay them on  
> top of the resolution dependent fourier ripples for a heavy atoms  
> electron density map. Any ideas?
> Thanks,
> Dave Chenoweth

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