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 later) 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 ----- 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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