[Chimera-users] Transparent Spheres

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 30 09:28:18 PDT 2009

Hi Drew,
No need to apologize, it is not a simple issue!

The "sphere" representation is the solid VDW surface, so just use that  
unless you actually wanted dots.  Since something can't be both sticks  
and spheres at the same time, you could do it by opening the structure  
twice and showing one as sticks and the other as spheres.  Then make  
the spheres a transparent color.  More details below....

However, I don't think this will look very good because you see all  
the sphere intersections.  Showing a transparent surface would look  
better.  The tricky part in that case would be getting surfaces that  
enclose the sets of atoms you want rather than the entire structure,  
where a given residue might only contribute a tiny scrap to the  
molecule's surface.

First, the transparent spheres example commands:

open 1zik
open 1zik
disp :tyr
rep sphere #1
colordef tyellow 1 1 0 .5
color tyellow #1

(or you could skip the colordef and just use "color 1,1,0,.5 #1" but  
sometimes it is more convenient to define a bunch of transparent  
colors first, or have a command file to do that, and then use them  

If you use the surface approach, it is not necessary to open the  
structure twice, and it is easier to just make the surface transparent  
without changing its color (see Actions... Surface menu and/or  
"surftransparency" command).  There are at least a couple different  
surface approaches.

(A) molecular surface, but then you must use surfcat to make the  
surface enclose just the sets of atoms you want:

open 1zik
disp :tyr
surf :tyr
(see that only the patches for those residues in the context of the  
whole surface are shown)
surfcat mytyrs :tyr
surf mytyrs

... and then color the surface and make it transparent as desired

(B) use "molmap" command to make a density map from specified atoms  
which is shown as an isosurface, but that would not automatically be  
at the VDW surface... you'd have to play with the contour level

open 1zik
molmap :tyr 2

and then play around with contour level and use various other options  
in Volume Viewer to adjust appearance (set color, make transparent,  
see "Features... Surface and Mesh Options" for smoothing etc.).  You  
can also use the "Actions... Surface" menu and command  
"surftransparency" on this kind of surface, at least in recent  
versions of Chimera.

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

On Sep 30, 2009, at 8:33 AM, Waight, Andrew wrote:

> Hello everyone again.
>                     I apologize for a potentially embarassing  
> question but is it possible to display sidechains as transparent  
> spheres with solid stick representation inside. Seeing as I also  
> can't find an image in the Chimera gallery where it is represented  
> as such, I am wondering if it is possible to individually color (and  
> set opacity) on spheres. I am also aware that vdw will create dots  
> of varying density, but is it alternatively possible to display vdw  
> as solid surface with opacity. Thanks to all for your patience.
>                                                                                                                      Drew
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